this page suggests the problem is due to (parts of) the zip not being compressed.

Did you set the desiredCompressionMethod to COMPRESSION_DEFLATED?

If that doesn't help, (short) working code that exhibits the problem may shed some light. Alternatively, you could try using an external command-line driven zip program instead of Archive::Zip.

update: I did some experimenting, and I've got nothing. I note that jar can be very picky about its input format, and that although I've used Info-ZIP on linux to create/modify some working jars, I've also run into problems with it (anecdotal - I's been a few years since I tried any of that). Conservative advice would be to unpack the jar however you like it, modify whatever you need, and use the jar program to create a new jar, since that at least should work.