I have had customers running snapmanager and I have never seen anything like this. As far as I know Snapmananger uses the the Exchange backup API so nothing should be different, except where the backup is stored and how it is stored.
It looks like this might be the issue. The snapshot API and the NTBackup do different things.
http://now.netapp.com/NOW/cgi-bin/bol?Type=Detail&Display=53144 I missed seeing this originally.
I think these folks were just surprised that none of the folks that helped them set everything up suggested that this might be a problem.
Since the bug mentions 2000 explicitly, I'm hoping that this does not affect 2003. If so, they might be willing to do the upgrade sooner rather than later to avoid having to do periodic cleanup at this stage.
Thanks for all the suggestions!