I have tried using a puppet from Photoshop and adding Puppet Pins. My program either freezes or does not mark the places where motion should occur. Any ideas?
Two things come to mind:
Puppet Tool can be the ONLY thing applied to a layer. You can't animate anything else. I don't think you can even parent it to another layer without breaking the Puppert Tool. Check for that.
Have you updated your OS recently? If you did, you may want to undo it. Microsoft pulled the latest OS 10 update over the weekend because it was such a dog and screwed up a lot of things -- that might apply to AE, too.