The new Terminal plugin allows you to peek into the Scheduler. I recommend that you start by upgrading that plugin. More info: http://forum.gpsgate.com/topic.asp?TOPIC_ID=12710
Now in SiteAdmin under System Tools -> Scheduled Tasks you can see if "Cleanup" is scheduled. If it is you know that and when this operation will run.
Under System Tools -> Queue Viewer you can search for _Cleanup commands. Those are the once that are executed to do the actual cleanup. By expanding the command in the search result, you can see which application, time period and operation which was made.
InnoDB, which is the MySQL database engine used by GpsGate will not shrink the database file, it will rather reuse space from deleted records to new inserted records.