Hi, You are probably suffering from the fact that XWin is running in a separate process from your .bat. If you wait until XWin is fully initialised and then run xmodmap's you will be OK.
See link below for the .bat I used to use, that waits for initialisation to complete (note that the log file has changed name) http://sources.redhat.com/ml/cygwin-xfree/2003-03/msg00125.html Colin
