I have not encountered this problem and do not want to set out to cause it either! It is probably a SQL Server bug.

I see that there is some evidence that once you have setup TDE on a server you may need to keep the server certificate and the Database Master Key (DMK) in the MASTER database even though you no longer have any databases setup for TDE. So if you have this problem with databases becoming suspect on restart you should try putting the server certificate and DMK back. Not really a problem to have them there if not being used.