This is not a Remote Buddy specific problem. In all shortness:

- OS X has built-in support for the Apple Remote (although a very limited one when compared to what you can achieve with Remote Buddy)

- each Mac with built-in IR receiver reacts either to all or only one Apple Remote (or, optionally, a selection of Apple Remotes if you use Remote Buddy)

- if you pair your remote with one computer but don't make any configuration changes on the other, both computers will still react to one and the same remote

- if you don't want a Mac to react to an Apple Remote, you can either disable the IR receiver - or - pair it with a *different* Apple Remote (both can be done at System Preferences > Security - or - in Candelair)

Hope that helps.

Best regards, 
Felix Schwarz