Not sure if you have had a resolution to this yet. We had an almost an identical problem. After months of investigation CommVault was able to provide us with some potential changes, which when we made along with some other little chages has made huge improvements in speed on a continual bassis.
Issue one: You LUN size is too big you need to reduce them from 3 to sub 2 TB, in our design we changed down to 1TB LUNS.
Issue Two: DeDuplication - this fragments the crap out of your 3TB LUN which effectively kills any level of performance on your SAN back to CommVault, again reduce LUN size and run an alternating Defrag process on your backup LUNS, we don't use the in built windows one as it takes too long, spend a little $$ its worth it as you can configure schedules and individual LUN policies for defraging.
Issue Three: Given your back end SAN are there times when reads and Writes are occuring, given they are SATA disks, any occurance like this is VERY VERY VERY bad and should be avoided like the plague.
Bascially DeDupe, hammers the crap out of the disk and leaves it an absolute mess so these little steps should help to ensure your performance stays good, it certainly helped us.