This problem was indeed reported some time ago and I've tested several zip files that were marked as bad using unzip.exe from info-zip.
Those archives have a truncated zip comment. The zip file is then considered as bad (read: corrupted) but can (may ?) still be extracted.
Open those archives and search for *.nfo files with funny timestamps and you'll know what other script has corrupted the zips while adding new files. As FTPServerTools said, "not every zip implementation is correct".
PS: I've marked this thread as fixed because this "problem" no longer exists in my current version.
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