I can't see any errors in the logs explaining why this would be the case.
Does it happen with all Zip files, or just this particular one?
Is the Zip file over 20MB? If so it won't like that. Maybe try splitting it into smaller files and see if we can identify the problem?
If the zip file isn't too huge, please could you email it to email@example.com and I'll see if I can reproduce the problem on our test site.