Bearclaw: Check where your registry value for your default SE:IV location is. Edit this string to match it's current location and it should resolve any patch issue. This happened to me because I kept making duplicate folders of the original install and then tried to apply the patch to them.
I'll try to duplicate this in one of my pbw games.
Weird. I have never seen a bug like this, even though i spent quire some hours with SE IV, though probably not by far as much as some other people in here did.