While the "inquiry" process to initially pair with a remote does 
definately have an effect on other BT software running on the Mac 
insofar as they can not run inquiries of their own at the same time 
or initiate connections during this time (not documented anywhere as 
far as I can recall - I just noticed this while writing the drivers), 
once the remote is paired with Remote Buddy, it's really just a plain 
Bluetooth connection and no special modes of operation (like 
inquiries or searching for known remotes) are entered anymore, so it 
should be in perfect harmony with all other connected devices.

I'll still try to reproduce, though.

Best regards, 
Felix