LyX sometimes tries to run the systemdir configure script as ::system("$systemdir/configure"); See LyX::queryUserLyXDir() (lyx_main.C) and Reconfigure() (lyx_cb.C).
Unfortunately, this doesn't work on Windows. Windows ascertains the type of the file simply from its extension, not from the first line #! /bin/sh magic that works under *nix. Thus, Windows screws up, interpretting the configure script as a batch file. See the output of `lyx -dbg init` that is stored in the lyx_init.txt file that I posted with the mail entitled: [PATCH 13x, 14x] starting LyX successfully under Windows. Two solutions present themselves. 1. Rename lib/configure as lib/configure.sh 2. Start the script as ::system("sh $systemdir/configure"); I suspect that weird autotool gremlins will jump up and bite me if I try (1). I'll try out (2) this evening. -- Angus