Firstly to get over your Exchange logs growing, simply do a NON Advanced Open File Agent Option (AOFO) backup of JUST the message store, with the flush exchange logs option.
If that doesn't work, then do a FULL backup of the ENTIRE exchange server (with flush logs option without AOFO it will complain, but you prob don't care about system files, jus in reducing your growing logs)
I've gone from 10d, and differential using AOFO which merrily copied both the open files on the system (C:\ drive) AND flushed the logs
to being forced to use 2 jobs, one nightly differential AOFO job which backs up everything BUT the exchange store, and another job which DOESN'T use AOFO and JUST backs up the Mailstore (with flush logs)
Just one of the many joys that 11d has brought me.