We actually have a very similar issue being the throughput is so slow. We disabled our antivirus software (Norton) realtime scanner not to scan backup files, and it seems to me it speed it up a bit. The next thing we are still working on is to defrag the disk, actually happening now and see if it makes any difference.
But at the end of the day, yes we do have a lot of small files to back up and this is reality. Are there any other options available to accomodate (speedup) this sort of environment, being a lot of small files ???
Rgds/KL