Hi, I was having the exact same problem.
Activation emails reached the users inbox and just sat there without ever being processed. The BB device would then just time out after a while.
However, this only affected new domain user accounts that were added to BES. Activating BB's using already existing domain user accounts always worked flawlessly.
After a truckload of fruitless attempts to solve the issue, I decided to restart ALL Blackberry Services on the server - and voila! It works perfectly fine now.
Unfortunately, I didn't monitor the users inbox while I was restarting the services. So I don't know which exact service was the culprit.
I hope this information helps some of you.