I've had that happen before. Sounds like you need to run the update again, I had to do that with PB2. Just run it again and you should be alright. One thing I've noticed that helps when updating, don't run it in the background, keep it at the front until finished, and make sure the computer can't sleep (click on the window once in a while) until finished.
I'm sure it's not designed to work like this, but it works this way for me. YMMV.