When I compare a Zipped folder or subfolder with a normal folder target, the comparison correctly identified the files to be copied. The synchronize operation appears to complete (the check marks on the source are switched off) but nothing is actually copied if older versions of the target files already exist. If nothing exists in the target, then a subset of the zipped source is copied. In the example below, the contents of the Languages folder are created at the top level of the target and top level source files (not visible in the screen grab, but present in the zip) are ignored.
I checked the online help for synchronize and can't see any restriction on Zips.