... Hrm, next time I get a chance to sit down in the CS lab and hammer away at it for a while (I currently only have a Linux box available to me without making a trip across campus) I'll try strace. As the previous poster suggested, I had already tried cygcheck, and all it spat back at me was SDL.dll, cygwin1.dll, and a bunch of standard Windows DLLs. Perhaps there's a compiler switch that I missed?
Have you considered the registry? Installing Cygwin updates the registry - it's where the mount points are recorded. If your app is using a POSIX-style path anywhere (eg /tmp/...) this would not be found, and if your app is dependent on the text/binary mount switches it would behave differently.
A quick check would be to temporarily rename your Cygnus Solutions registry keys (in HKLM/Software and HKCU/Software), or else use mount to experiment.
-- Cliff
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