I could no longer reproduce it. But here is the later part of the debug when I tried to enable the debug in the *.trn file when I was still able to reproduce it.
132 0132132132132132 0132
132 0132132132132132 0132
132 0132132132132132 0132
132 0132132132132132 0132
132 0132132132132132 0132
LegalDrop: 2 @ 5,3)
Parsed game start '[Event "Edited game"]' (39)
Parsed PGNTag: [Event "Edited game"]
Parsed PGNTag: [Site "MAKRO-PC"]
Parsed PGNTag: [Date "2013.08.06"]
Parsed PGNTag: [Round "7"]
Parsed PGNTag: [White "-"]
Parsed PGNTag: [Black "-"]
Parsed PGNTag: [Result "*"]
Parsed PGNTag: [Variant "shogi"]
recognized 'shogi' (-1) as variant shogi
Parsed PGNTag: [FEN "rbsgk/4p/5/P4/KGSBR[-] w 0 1"]
shuffleOpenings = 0
Parsed PGNTag: [SetUp "1"]
Parsed PositionDiagram: {--------------
r b s g k
. . . . p
. . . . .
P . . . .
K G S B R
white to play
--------------}
Load Game
Parsed Gc2 into b1c2 virgin=0,0
Parsed Bc4 into b5c4 virgin=8,0
Parsed Comment: {+0.68/18 5:51}
Append: in='{+0.68/18 5:51}' 0
Parsed Gb2 into c2b2 virgin=8,8
Parsed Comment: {-0.24/18 7:20}
Append: in='{-0.24/18 7:20}' 0
Parsed Sd4 into c5d4 virgin=8,8
Parsed Comment: {+0.20/17 1:55}
Append: in='{+0.20/17 1:55}' 0
Parsed Bc2 into d1c2 virgin=8,18
Parsed Comment: {-0.36/18 4:39}
Append: in='{-0.36/18 4:39}' 0
Parsed Rb5 into a5b5 virgin=28,18
Parsed Comment: {+0.12/17 4:04}
Append: in='{+0.12/17 4:04}' 0
Parsed Sd2 into c1d2 virgin=28,1c
Parsed Comment: {+0.16/16 2:31}
Append: in='{+0.16/16 2:31}' 0
Parsed Ra5 into b5a5 virgin=38,1c
Parsed Comment: {-0.08/16 4:07}
Append: in='{-0.08/16 4:07}' 0
Parsed Rc1 into e1c1 virgin=38,1c
Parsed Comment: {+0.16/16 2:29}
Append: in='{+0.16/16 2:29}' 0
Parsed Rb5 into a5b5 virgin=78,1c
Parsed Comment: {-0.20/16 1:53}
Append: in='{-0.20/16 1:53}' 0
Parsed Ga3 into b2a3 virgin=78,1c
Parsed Comment: {+0.80/16 3:46}
Append: in='{+0.80/16 3:46}' 0
Parsed Be2 into c4e2 virgin=78,1c
Parsed Comment: {-0.44/16 2:30}
Append: in='{-0.44/16 2:30}' 0
Parsed Bb3 into c2b3 virgin=78,1c
Parsed Comment: {+0.44/17 3:50}
Append: in='{+0.44/17 3:50}' 0
Parsed Gc5 into d5c5 virgin=78,1c
Parsed Comment: {-0.32/17 4:59}
Append: in='{-0.32/17 4:59}' 0
Parsed Rxc5+ into c1c5+ virgin=78,3c
Parsed Comment: {+0.28/16 1:52}
Append: in='{+0.28/16 1:52}' 0
Parsed Rxc5 into b5c5 virgin=78,3c
Parsed Comment: {-0.20/17 2:09}
Append: in='{-0.20/17 2:09}' 0
Parsed Gb4 into a3b4 virgin=78,3c
Parsed Comment: {+0.76/16 3:12}
Append: in='{+0.76/16 3:12}' 0
Parsed Bd1+ into e2d1+ virgin=78,3c
Parsed Comment: {-0.68/16 4:10}
Append: in='{-0.68/16 4:10}' 0
Parsed Bxd1 into b3d1 virgin=78,3c
Parsed Comment: {+1.20/16 4:57}
Append: in='{+1.20/16 4:57}' 0
LegalDrop: 69 @ 4,0)
LegalDrop: 69 @ 4,0)
Parsed R@c1 into R@c1
Parsed Comment: {-1.28/16 3:33}
Append: in='{-1.28/16 3:33}' 0
LegalDrop: 9 @ 3,0)
LegalDrop: 9 @ 3,0)
Parsed G@b1 into G@b1
Parsed Comment: {+1.16/17 5:29}
Append: in='{+1.16/17 5:29}' 0
Parsed Rxd1+ into c1d1+ virgin=78,3c
Parsed Comment: {-1.16/16 3:34}
Append: in='{-1.16/16 3:34}' 0
Parsed Gxc5 into b4c5 virgin=78,3c
Parsed Comment: {+1.16/15 3:15}
Append: in='{+1.16/15 3:15}' 0
LegalDrop: 68 @ 3,1)
LegalDrop: 68 @ 3,1)
Parsed B@b2 into B@b2
Parsed Comment: {-1.16/14 2:20}
Append: in='{-1.16/14 2:20}' 0
Parsed Kxb2 into a1b2 virgin=78,3c
Parsed Comment: {+1.72/1}
Append: in='{+1.72/1}' 0
Parsed +Rxd2 into d1d2 virgin=7c,3c
Parsed Comment: {-1.12/14 4:28}
Append: in='{-1.12/14 4:28}' 0
Parsed Ka1 into b2a1 virgin=7c,3c
Parsed Comment: {+1.04/14 4:11}
Append: in='{+1.04/14 4:11}' 0
Parsed Sxc5 into d4c5 virgin=7c,3c
Parsed Comment: {-1.08/13 2:18}
Append: in='{-1.08/13 2:18}' 0
LegalDrop: 2 @ 3,1)
LegalDrop: 2 @ 3,1)
Parsed B@b2 into B@b2
Parsed Comment: {+1.12/13 7:55}
Append: in='{+1.12/13 7:55}' 0
LegalDrop: 71 @ 5,3)
LegalDrop: 71 @ 5,3)
Parsed S@d4 into S@d4
Parsed Comment: {-1.16/13 4:00}
Append: in='{-1.16/13 4:00}' 0
LegalDrop: 3 @ 3,4)
LegalDrop: 3 @ 3,4)
Parsed R@b5 into R@b5
Parsed Comment: {+1.12/13 2:06}
Append: in='{+1.12/13 2:06}' 0
LegalDrop: 75 @ 5,4)
LegalDrop: 75 @ 5,4)
Parsed G@d5 into G@d5
Parsed Comment: {-0.96/15 3:58}
Append: in='{-0.96/15 3:58}' 0
LegalDrop: 2 @ 2,4)
LegalDrop: 2 @ 2,4)
Parsed B@a5 into B@a5
Parsed Comment: {+1.24/13 1:58}
Append: in='{+1.24/13 1:58}' 0
Parsed +Rd3 into d2d3 virgin=7c,3c
Parsed Comment: {-1.08/15 3:15}
Append: in='{-1.08/15 3:15}' 0
Parsed Be1+ into a5e1+ virgin=7c,3c
Parsed Comment: {+0.84/17 4:08}
Append: in='{+0.84/17 4:08}' 0
Parsed Sc4 into c5c4 virgin=7c,3c
Parsed Comment: {-0.88/16 2:23}
Append: in='{-0.88/16 2:23}' 0
Parsed Rb4+ into b5b4+ virgin=7c,3c
Parsed Comment: {+0.96/16 6:05}
Append: in='{+0.96/16 6:05}' 0
Parsed +Re3 into d3e3 virgin=7c,3c
Parsed Comment: {-0.60/16 4:21}
Append: in='{-0.60/16 4:21}' 0
Parsed +Bd1 into e1d1 virgin=7c,3c
Parsed game end: {-0.20/16 4:29}
*
GameEnds(29, -0.20/16 4:29, 3)
ForwardInner(39), current 0, forward 39
PauseEvent(): pausing 0
LoadGame(): on exit, gameMode 7
StartChildProcess (dir="../SjaakII") SjaakII-64.exe
nice engine proc to 10
532 >first : xboard
protover 2
532 <first : Sjaak II version 1.4.1 (x86_64)
532 <first : Type 'help' for a list of commands and help topics
532 <first : 8r n b q k b n r
532 <first : 7p p p p p p p p
532 <first : 6
532 <first : 5
532 <first : 4
532 <first : 3
532 <first : 2P P P P P P P P
532 <first : 1R N B Q K B N R *
532 <first : a b c d e f g h
548 <first : #[Chess] 0w>
548 <first : feature setboard=1 time=1 sigint=0 colors=0 highlight=1 ping=1 memory=1 analyze=1 pause=1 nps=1 sjef=1 myname="Sjaak II 1.4.1" myversion="[1.4.1 (x86_64)]" variants="seirawan,shatar,makruk,shatranj,sittuyin,crazyhouse,chessgi,asean,ai-wok,super,spartan,pocketknight,kingofthehill,knightmate,berolina,losalamos,micro,capablanca,gothic,embassy,greatshatranj,courier,grand,opulent,omega,minishogi,shoshogi,shogi,torishogi,xiangqi,chess960,fischerandom,fischerrandom,nocastle,wildcastle,great,caparandom,minisho,5x5+5_shogi,tori,7x7+6_shogi,sho,9x9+0_shogi,king-of-the-hill,fairy,8x8+0_fairy,8x8+6_fairy,8x8+1_fairy,6x6+0_fairy,5x5+0_fairy,10x8+0_fairy,12x8+0_fairy,10x10+0_fairy,12x12+0_fairy,5x5+5_fairy,9x9+0_fairy,9x9+8_fairy,7x7+6_fairy,9x10+0_fairy,normal"
548 >first : accepted setboard
548 >first : accepted time
548 >first : accepted sigint
548 >first : accepted colors
548 >first : accepted highlight
548 >first : accepted ping
548 >first : accepted memory
548 >first : accepted analyze
548 >first : accepted pause
548 >first : accepted nps
548 >first : rejected sjef
548 >first : accepted myname
548 >first : rejected myversion
548 >first : accepted variants
548 <first : feature option="Variant fairy selects -combo chess (8x8+0) /// seirawan (8x8+0) /// shatar (8x8+0) /// makruk (8x8+0) /// shatranj (8x8+0) /// sittuyin (8x8+6) /// crazyhouse (8x8+6) /// chessgi (8x8+6) /// asean (8x8+0) /// ai-wok (8x8+0) /// super (8x8+0) /// spartan (8x8+0) /// pocketknight (8x8+1) /// kingofthehill (8x8+0) /// knightmate (8x8+0) /// berolina (8x8+0) /// losalamos (6x6+0) /// micro (5x5+0) /// capablanca (10x8+0) /// gothic (10x8+0) /// embassy (10x8+0) /// greatshatranj (10x8+0) /// courier (12x8+0) /// grand (10x10+0) /// opulent (10x10+0) /// omega (12x12+0) /// minishogi (5x5+5) /// shoshogi (9x9+0) /// shogi (9x9+8) /// torishogi (7x7+6) /// xiangqi (9x10+0) /// chess960 (= chess) /// fischerandom (= chess) /// fischerrandom (= chess) /// nocastle (= chess) /// wildcastle (= chess) /// great (= greatshatranj) /// caparandom (= capablanca) /// minisho (= minishogi) /// 5x5+5_shogi (= minishogi) /// tori (= torishogi) /// 7x7+6_shogi (= torishogi) /// sho (= shoshogi) /// 9x9+0_shogi (= shoshogi) /// king-of-the-hill (= kingofthehill)"
548 >first : accepted option
548 <first : feature option="Mate search -combo Disabled /// *Enabled for drop games /// Enabled"
548 >first : accepted option
548 <first : feature option="Level -combo Clueless /// Random /// Static /// *Normal"
548 >first : accepted option
548 <first : feature option="MultiPV -spin 1 1 256"
548 >first : accepted option
548 <first : feature option="Draw offer threshold -spin 0 0 1000"
548 >first : accepted option
548 <first : feature option="Moves before draw offer (0 to disable) -spin 0 0 1000"
548 >first : accepted option
548 <first : feature option="Resign threshold -spin 500 100 16000"
548 >first : accepted option
548 <first : feature option="Moves before resigning (0 to disable) -spin 0 0 1000"
548 >first : accepted option
548 <first : feature option="Randomise opening moves -spin 10 0 40"
548 >first : accepted option
548 <first : feature option="Random amplitude (0 to disable) -spin 20 0 100"
548 >first : accepted option
548 <first : feature option="Send 'piece' descriptions -check 1"
548 >first : accepted option
548 <first : feature option="Mark holes in board -check 1"
548 >first : accepted option
548 <first : feature option="List user-defined variants before buildin variants -check 1"
548 >first : accepted option
548 <first : feature option="Report fail low -check 0"
548 >first : accepted option
548 <first : feature option="Report fail high -check 0"
548 >first : accepted option
548 <first : feature option="Claim repetitions -check 1"
548 >first : accepted option
548 <first : feature option="Send O-O/O-O-O for castling -check 1"
548 >first : accepted option
548 <first : feature option="Remember evaluation parameter file -check 0"
548 >first : accepted option
548 <first : feature option="Variant 'normal' is -string chess"
548 >first : accepted option
548 <first : feature option="Set variant alias -string "
548 >first : accepted option
548 <first : feature option="Variant configuration file -file "
548 >first : accepted option
548 <first : feature option="Evaluation parameter file -file "
548 >first : accepted option
548 <first : feature done=1
548 >first : accepted done
563 >first : memory 132
563 >first : new
random
563 >first : variant 5x5+5_shogi
563 >first : level 0 1 1
563 >first : post
563 >first : hard
563 >first : easy
563 >first : ping 1
Feeding position and moves 0 through 39 to first chess program
563 >first : force
write FEN 50-move: 0 39 0
e0. p=-1
e1. p=-6
e2. p=-6
e3. p=-6
e4. p=-6
e5. p=-6
e6. p=-6
e7. p=-6
e8. p=-6
e9. p=-6
e10. p=-6
e11. p=-6
e12. p=-6
e13. p=-6
e14. p=-6
e15. p=-2
e16. p=-2
e17. p=-6
e18. p=-6
e19. p=-2
e20. p=-6
e21. p=-6
e22. p=-2
e23. p=-2
e24. p=-6
e25. p=-2
e26. p=-2
e27. p=-6
e28. p=-2
e29. p=-6
e30. p=-6
e31. p=-6
e32. p=-6
e33. p=-6
e34. p=-6
e35. p=-6
e36. p=-6
e37. p=-6
e38. p=-6
e39. p=-6
563 >first : setboard rbsgk/4p/5/P4/KGSBR[-] w 0 1
feedMoves
563 >first : b1c2
563 >first : b5c4
563 >first : c2b2
563 >first : c5d4
563 >first : d1c2
563 >first : a5b5
563 >first : c1d2
563 >first : b5a5
563 >first : e1c1
563 >first : a5b5
563 >first : b2a3
563 >first : c4e2
563 >first : c2b3
563 >first : d5c5
563 >first : c1c5+
563 >first : b5c5
563 >first : a3b4
563 >first : e2d1+
563 >first : b3d1
563 >first : R@c1
563 >first : G@b1
563 >first : c1d1+
563 >first : b4c5
563 >first : B@b2
563 >first : a1b2
563 >first : d1d2
563 >first : b2a1
563 >first : d4c5
563 >first : B@b2
563 >first : S@d4
563 >first : R@b5
563 >first : G@d5
563 >first : B@a5
563 >first : d2d3
563 >first : a5e1+
563 >first : c5c4
563 >first : b5b4+
563 >first : d3e3
563 >first : e1d1
579 <first : # New game 'Chess'
579 <first : # New game 'minishogi'
579 <first : setup (P.BR.S...G.+.++.+Kp.br.s...g.+.++.+k) 5x5+5_shogi rbsgk/4p/5/P4/KGSBR [-] w 0 1
579 <first : piece P& fWf@4
579 <first : piece S& FfW
579 <first : piece B& B
579 <first : piece R& R
579 <first : piece G& WfF
579 <first : piece K& K
579 <first : piece +P& WfF
579 <first : piece +S& WfF
579 <first : piece +B& BW
579 <first : piece +R& RF
GameEnds(29, -0.20/16 4:29, 2)
results = '+-+---+----++--++++-+--++----++---+++--++-+----++-+--+--+++++-+-+-+--+-++--+-++----+--------+++-+--++-+--+--+--+-++++-+---+---+--------+--+-----+++---+-+++------++-----+-+--+---++-+--++-+--++++--+* +- -+ '
Shokidoki UEC9+ 32bit\012TJshogi 5x5 0.19 32bit\012Sjaak II v1.4.1 64bit\012Lima v4.0 64bit\012CrazyWa 1.0.2 32bit\012NebiyuAlien 1.46 32bit\012
pick next game from '+-+---+----++--++++-+--++----++---+++--++-+----++-+--+--+++++-+-+-+--+-++--+-++----+--------+++-+--++-+--+--+--+-++++-+---+---+--------+--+-----+++---+-+++------++-----+-+--+---++-+--++-+--++++--+ +- -+ ': 197
Reserved, next=197, nr=196
ScheduleDelayedEvent: event already scheduled
8703 >first : quit
I think Martin mentioned he found an issue with the Sjaak was that already addressed?, it could be related to this.