I have never used RR. SKINbedder emulates keyboard presses. Whichever window has focus will recieve them.
Are you talking about the RR buttons not sending keys properly until you click the map once? If so, I would try adding "Focus(iGMap)" to the end of your startup script. That should fix it.
B8: I was planning on adding Hot-Key scripts a long time ago. I never spent the time to figure out how to intercept key presses though.