Probably alot of key steps got skipped because the database wasn't ready with all the fields yet from the first altertable.
It's definately usually bad to run an altertable more than once.
I would restore a backup and run the altertables - one at a time - in order to ensure nothing got screwed up.
That 6.1-6.2 one was a doosey - and if it gets run more than once you'll lose Private Messages and favorites etc...
