There are two reasons why a differential is taken instead of the Fast Incremental. They are a dirty shutdown and/or missing incrementals. You stated that the system rebooted over night, was it planned? Is there event that precipated the reboot?
We have had a few rare cases where shutdowns actually BSOD during the process but now one very notices because the system is set to auto reboot. I would manually test this to see if the reboot is really clean or not. Check the event logs for any messages related to dirty or bad shutdowns. Also, check to see if you can manually force a fast incremental after a simple reboot.
If there was a missing backup file after the USB drive was plugged back in, then that could cause the issue as well.
Send us your log files for the time that the differential was taken and we should be able to quickly see why it was taken instead of a fast incremental. You log files can be found in c:\program files\storagecraft\shadowprotect\logs.
STC