It might still have to do with backups, depending on what's happening.
But let me just get a clear understanding of this machine.
So, this is a workstation, rather than a server, that has RE and the BBNC plugin, which is used exclusively (or, at least the plugin is exclusive to this machine) for the purpose of bringing transactions into The Raiser's Edge.
Assuming that's the case:
-Do you always leave the plugin running, or do you log out of the machine (or even just RE/BBNC Plugin)
-Do you have any other machines that you could put the plugin on and see if it happens there as well?
K