This happens if you have ZipMagic from Aladdin Systems (to my knowledge it came from Ontrack before) installed. ZipMagic displays all zip files as folders, and even denies other applications access to the real zip file.

To allow another application direct access to zip files, ZipMagic has a setting somewhere on its Options page. You need to add SpybotSD.exe there. Instructions from kind user follow:

1. Open the ZipMagic properties,
2. Click on the icon Applications at the left.
3. Check the option These applications see Zip files as files,
4. Press the Add... button, and
5. Select the SpybotSD executable in the dialog appearing (usually C:\Program files\Spybot - Search & Destroy\SpybotSD.exe).

This will tell ZipMagic to allow Spybot-S&D access to zip files again.