In the MySQL setup, if you forget to set the database schema to MyISAM AFTER you try to run REPET, you must go back and delete the tables in MySQL and restart from scratch. The syntax is on google.
Additionally, I have been receiving empty outputs from the GROUPER clustering program. Not sure if this is related to my fragmented assemblies, but you can try to troubleshoot by running the commands yourself without the SGE system by examining the system command calls in the python script created inside of the working directory.
It is worth the trouble, at least in regards to the model organism reference I have succeeded with. 4x the amount of repeats in the library than from RepeatModeler.