Nope, didn't move/rename files. Does it make a difference if the mod is enabled or not? I can't imagine that it would, but...Just checked over the script and ran it again against the Matrix version, works every time. I wish I knew what was wrong, but for some reason the script is failing to remove those files on some machines. I'm assuming that you didn't rename the folder or change anything in there. I'll keep looking, but thanks.
My game is installed at C:\Matrix Games\Scourge of War Waterloo, so I should have any of the privilege issues you get if the game was in Program Files. FWIW, I didn't run the patch as Administrator.
The only other guy over at Grogheads that I know installed the patch had the same issue. It didn't remove the files for him, either.
Weird problem. Let me know if there's any other means of testing I can try for you.