Hi Stephen,
Various expungers and other sceduled jobs run (by default) during the hours of 1:00am and 5:00am on the Control Center which might impact the usage of resources, but those jobs only run on an appliance that hosts the Control Center function. Is the Inbound scanner you mentioned a Scanner-only appliance or it has the Control Center functions as well?
Without looking at the diagnostics that capture debug level logs during the problem period, it's hard to tell what's the root cause of the issue you are experiencing.
I would suggest opening up a case with support, if you have not already done so.
Regards,
Adnan