I've had problems with Paperport 11 freezing up (not responding, crashing, whatever). Turns out that my problem is that the thumbnail files (which Paperport names "PP11Thumbs.ptn" and "PP11Thumbs.ptn2") were corrupted. I exited out of Paperport (it was not responding anyway), went into the directory where those files were stored, and deleted them both.
All that does is, when Paperport 11 starts up and you go into that directory, it will take a few extra seconds while it rebuilds the thumbnails. However, it won't freeze up anymore after that.
I have to agree with the many people who are very unhappy with the fact that the program crashes, but this is a work-around until Nuance fixes the problem. If that ever happens.