Are you also using Cygwin? Could it be that you have two versions of Perl (including related utilities) conflicting?

On one PC at home, I have Perl for both Windows (Strawberry) and Cygwin and I don't think that I ever had any such problems, and I don't see it very likely, but it might happen sometimes, who knows? At least the symptoms you are reporting (with Unix path types) give the impression that it could be something like this.

Update: I had not seen your answer saying that you are also running Cygwin when I wrote this post asking the question. I was disturbed by a phone call when writing this and I did not think about refreshing the thread before posting. Sorry for asking somewhat obsolete questions.