It sounds like you are having a problem similar to this:
I have a feeling that, like in that situation, you have files left from a previous failed installation which are "locking" you out from running an update script again until they are out of the way...
I hope that you have backups before even if you find out what they are and are able to run the rest of the script there is a possibility that your installation might be hosed..
Good luck and have a nice day!
PS: Personally I have always had better luck running the update scripts manually...