With the CLEAN_TIMEOUT property set to 10 minutes, 10 minutes is too low of a setting and not recommended. Typically, it is set to a value to prevent the Cleanup Agent from running too long.
How that property comes into play with the Cleanup Agent is that it runs each cleanup task in order. The cleanup process contains several tasks: cleaning up BO records, workflow instance history, doc tables, etc. Once a task is complete, it looks at the current running time, compares it to the property, and decides whether or not to continue with the next task. With that said, it doesn’t even look like it’s honoring the property at all, based on your logs, because it should have ended at this line:
2016-09-01 22:28:58,117 INFO [com.tririga.platform.dataconnect.JobControlManager](PlatformMaintenanceScheduler) DataConnect Tables Clean up completed at Thu Sep 01 22:28:58 CDT 2016 deleted 0.