I've had another thought regarding this. The indexing component of CPS causes us a lot of problems. It uses a lot of memory and constantly falls behind, even on a dual xeon CPU server with a fibre attached storage.
We actually have no need for Backup exec retrieve and the search capabilities so I have recently installed CPS without indexing. I'm hoping that indexing is also causing some of the problems with backing up the CPS data, as it is constantly accessing files. Time will tell as I haven't run a tape backup of this data yet...