Databases in Suspect state after enabling TDE
For the 3 suspect databases can you check the log files referred to in sys.master_files physically exist on disk and have the same access permissions as the other working database log files? Just that one of the error messages you posted said the log file is missing, and unless it's a red herring, that would make their problem separate to your TDE issues and explain the suspect status.

I've noticed this in your log: 04/13/2016 15:18:23,spid61,Unknown,Database SuspectDb was shutdown due to error 9001 in routine 'XdesRMReadWrite::RollbackToLsn'. 

This can happen if there are transactions in the log file which cannot be rolled back due to a lack of space, forcing the db into suspect mode. Can you confirm the underlying disk has free space, and also that you have not set and hit a size limit on that database's files (e.g. that auto-grow is enabled and set to grow by a sane fixed amount)?