I have a similar problem that turns out to be some rather inefficient code that truncates several very large tables and reloads ALL of the data from an AS 400 every bloody night. Folks are in the process of repairing the code for performance and I'm in the process of moving the tables to a dedicated database in the SIMPLE recovery mode and to a separate set of disks not on the SAN.

My recommendation would be to run a server side trace for anything that takes too long or writes too much data. It's something that should be done once in a while even if it's not affecting quorum size.