I tried a normal uninstall (should do the same thing as a silent uninstall, I just don't have that set up) and can't reproduce the problem so far.
Is your silent uninstall setup using the current setup.exe etc. or an old one?
The registry settings in the zip for How to manually remove Explorer Replacement settings should fix things if the uninstall didn't restore the old registry settings for some reason. (Permissions, perhaps?)
Sometimes the Windows shell takes a few seconds after changing the registry before it behaves differently, as it seems to cache some of the involved settings, but after 10 seconds or so it should see the change.