I had the same problem and it seemed to be related to apps starting up via "reopen windows upon startup." Sometimes if I waited long enough a bunch of windows would pop up and I was back in business. In other cases, just rebooting over and over until it eventually worked. Since then I have changed my system to use a DSDT and haven't had the problem since.
ETA: I always unchecked reopen windows, for some reason it didnt always take I guess.