When the PeriodicRunner gets shut down during clean shutdown, the shutdown will stall if an existing Periodic Job is running and hanging. Shut down of the FlowControlTicketRefresher job can cause global IX lock acquisitions to hang (see
SERVER-41345). Since the _minOfCheckpointAndOldestTimestampListener job takes a global IX lock, if the FlowControlTicketRefresher shuts down while the _minOfCheckpointAndOldestTimestampListener is waiting on the IX lock acquisition, shutdown can still stall.
A fix for this is to move the bypass handling of Flow Control ticket acquisitions to occur before the PeriodicRunner shutdown.