"please wait while Windows configures..." comes up when unrelated exe runs

We have recently installed BusinessObjects Enterprise XI 3.1 SP2 on a Windows Server 2003 R2 SP2 server.

Since we have done this, whenever we run an exe that is completely unrelated to BOXI, we are presented with a dialog:

top blue line of dialog: BusinessObjectds Enterpsie XI 3.1 SP2

within dialog itself it says: Please wait while windows configures BusinessObjects Enterprise XI 3.1 SP2

and there is a cancel button.

I have tried running a repair, then a reboot, but still have the same issue.

Help!