erm i dunno, the only problem i had with GOTY and thepatch was that what you mentioned about the pbo and a damn registry setting lol, it thought that my addons folder in my base ofp folder on my comp was actually the base folder itself lol dumb computer, ill try and look into it for you though, the only thing i can suggest is move all ur addons and custom missions and d/l mission somewhere else (just as a precaution), uninstall GOTY then re-install it and then move your addons etc back into their proper files.
once the patch starts installng , dont open anything, leave it completely alone for 10-15 minutes, make a brew, chill out, relax and let it do its work and come back to it in 15 mins that kept happening to me it looked like it froze when i opened a folder but on the next attempt i didnt open the folder and it installed fine