Had a similar problem that involved FillDB.
The issues was traced to BigFix runningits nightly DB maintenance job at about midnight AND our BES Computer Removal task via BES Admin Tool was configured to run exactly at midnight.
No issues before 9.5.11 but shortly after the upgrade, the console would show all grey, the FillDB bufferdir was loaded, but FillDB was just not inserting those reports. Restarting the FillDB service remedied that and everything went back to normal.
Per our DBAs that are in charge of maintaining BFEnterprise, they said the system resources would hit 100% until FillDB was restarted. Tracked the issue down in the logs to about when the maintenance jobs ran. So changed the time of BES Computer removal job and we haven’t had the issue since (going on a week or so).
Up until this upgrade, we never had this issue. However, the logs showed DB connection issues around the times the jobs ran so FillDB seemingly was able to recover. Why that stopped in 9.5.11, I would like to know if I had more time to dig.