See strace/truss. It's a runtime call monitor for Perl, to find out where the problem is.

failed to fetch initial working directory

Is this the exact error message you get? I have a feeling that it's an issue with threading (you didn't mention in your post you use threads). Maybe you should post more code so we can take a look at it.

In reply to Re^3: rmtree() is failing after some time by dHarry
in thread rmtree() is failing after some time by KristinaBurden

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