On a different note, the article I posted states that issues with the sem5.log file growing especially large were meant to have been resolved in SEP12.1RU1MP1.
As you're now on SEP12.1RU2, can you check your DB maintenance settings and ensure truncation is enabled? If the logs are filling up so quickly that the default "Every 4 hours" truncate job is insufficient to keep the sem5.log file at a manageable size, then consider increaing the frequency of the task (perhaps every 2 hours).
If you wish to verify if SEPM's attempt to truncate is failing, then you may wish to run the steps in the below article the next time the log starts to get large
http://www.symantec.com/docs/TECH171546
This runs a truncate outside of SEPM, to help you troubleshoot one of the possible reasons the log is so large.