I don't know a thing about Archive::Zip, but if you're having problems extracting the same thing twice into two different places, why not extract the whole archive in to a throw away location (/tmp comes to mind) and just copy what you need to wherever you need it. You can make as many copies as you like. When you're done making copies, just delete the temp location and call it a day.

Yes, this is an inelegant solution, but it should be easy to implement.

- doug