Threading problems are notoriously difficult and on top of that Perl's implementation is probably still buggy. It's very hard to give you a helpful answer without seeing the code of the script and the template(s).
I think the best thing for you to do is to cut the offending program back to the smallest example that still demonstrates the bug. If the problem isn't clear by then, feel free to post the code here for people to look at. I'm sure the monks will be happy to help you out.
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