Are you using Cygwin Perl, or Perl for Windows (Active Perl)? It shouldnt matter, but it might.

Why are you using -e? You care if the file exists, but not if you have access to it? You tried using -r (for readable)?

I'm wondering if there is some sort of quirk about access to the directories the files are contained in.. Perl probably read the directory rather than the file to check if it exists.

The other thing you can try, is to actually open the file - and see if that fails.