You're allocating two different files, but both are ultimately being written to by Archive::Zip. So, again: You have a permissions problem. I don't see any problem whatsoever with the module at this point.
To debug this, both snippets should try to write to the same filename in the same directory. If you can do that and *still* have one work and one not, then we have somthing interesting...
Update:
In case you're confused, it looks like the first snippet is writing to "/caralan_com/system/proofing/cam_proofs/steve/live/flunk2.txt".
The second is writing to "/delme/$proofstem.zip"
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