Although corruption like this will certainly occur on a Windows box, binmode should be optional (albeit good practice) on Linux.

I had to do quite a bit of work to tidy up this code to make run though:

• You are using >> to update your archive. Are you very sure you want to append?
• Your "warn( print" style will see warnings printing "1" as this will likely be the result of the print

I managed to massage your code into something that works (in 5.12.4) on linux without binmode. Also consider upgrading Perl as V5.8 is ancient. I would suggest trying to create a very simple example that zips up, and the unzips a single file. If that still fails, post your simplified code