Thanks for sharing your findings.
Before posting, please read how to report bug or request support effectively.
Bug reports without an attached log file are usually useless.
If I just make a dummy(invalid) zip file with notepad WinSCP complains and tell that it's an invalid zip file. Guess it wouldn't tell that unless it actively tries to unpack the file?
.zip.folder, you can try to exclude those auto-extracted folders from the synchronization:
synchronize remote -filemask=|*.zip.folder/ -preservetime -mirror -delete \\SOURCE\C$\MDT /