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Thanks for asking.
Currently, the Boxee Remote is not supported by Remote Buddy.
Since the Boxee Remote essentially is a keyboard sending (mostly) regular, widely used key strokes and you seem to be assigning these as hotkeys to the HotKey Remote, you're facing the same problem as another user (search for "Virtual Keyboard conflict Apple Remote" for an explanation of mine - and why this can't be made to work).
In essence:
If you define f.ex. a cursor key or return key as a hotkey for HotKey Remote, whenever Remote Buddy needs to send a cursor or return key to control an application (which it needs to do often), the keystroke will not reach the application, but be intercepted by OS X itself and re-routed to Remote Buddy, which - after your configuration changes - has registered these keys as hotkeys.
Best regards,
Felix Schwarz