Sounds like something to do with the Software Manager, which is new for ePO 4.6.
Specifically a failure to validate product_strings.xml.tmp
Beyond that hard to pin it down, you might see more specific errors in the ePO log files from the time.
For info on ePO logging see McAfee support article:
PD23209 - ePolicy Orchestrator 4.6 Log File Reference Guide
Thanks Rackroyd, i will have a look at the logs, its odd as it doesnt seem to happen every night though