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OK, I've updated Winboard to version 4.4.0 (there was some minor tweaking I had to do to get it to compile in the version of MinGW/MSYS I use; notably there is no included help file) and was having problems with one side or the other losing on time unless I

• Gave each side 40 seconds to do 40 moves (too slow for what we're doing)
• Disabled pondering with -xponder

Here is the shell script I currently use for having Joker80 play itself:

#!/bin/sh

SECS=10

while : ; do

        winboard.exe -noGUI -xanimate -cp -fcp joker80.exe -scp joker80.exe \
          -boardSize middling -xponder \
          -variant capablanca -lpf schoolbook.fen -tc 0:${SECS} -mps 40 \
          -autosave -sgf game-${SECS}sec-40moves-$(date +%s).pgn -mg 10

        sleep 1

done

While there still is the occasional game won on time, most of the time the game ends in checkmate or draws by repetition.

Note that I also hacked backend.c to remove the popup that tells you the match results at the end of a match.