The latest Winboard version (4.5.2) leaves a file called winboard.ini inside %APPDATA% after it is run.
Tested on Win XPSP3 clean Virtualbox machine as admin.
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Were you running it from path with a space in it? If so, if you replace the WinBoardPortable.ini file with this does it fix it? It appears to work on my end.
Sometimes, the impossible can become possible, if you're awesome!
I can confirm that this fixes a different (maybe similar?) bug that prevents WinBoard Portable from properly running in a path with spaces. I can't reproduce the leftover file though.
http://portableapps.chrismorgan.info/irc/logs/?t=2012-08-17#T18-59-55
WinBoard Portable's installer also needs an update, so I'll package this up and send it.
This is fixed in 4.6.2
Sometimes, the impossible can become possible, if you're awesome!