There was a post over in the patch thread of a user with the same problem. He did a fresh reinstall of the game, then applied the patch, and all was good.
here's the thread:
http://www.ootpdevelopments.com/boar...=148133&page=3
Now, I have a mac. I beta tested on a mac, and I have not ever had this problem in the numerous times i have patched. But, I always install it do the default locationi in the applications folder. Is it possible that all of you that are experiencing this problem have the game in a "custom" location, and not setting that "custom" location when patching? Or, have some of you installed the game with complete defaults and are still seeing this issue?