I used to have this similar problem with iGuidance and RR on my old laptop/carpc, too. I used iGKeys for the keyboard shortcuts. What happened was that the first time RR and iGuidance starts up, everything works perfectly. iGuidance responds to every button pushed. Then if I open a web browser, either FF or IE, and then go back to the iGuidance skin, buttons no longer work. It's very weird. I was able to recreate it every time but I thought it was just my computer acting up.
So I ended up with a crappy solution. I use my RR buttons to send commands to Girder, which in turns, sends keyboard shortcuts back to iGuidance. My buttons are a little less responsive but it does work.
Hey liquid_smoke, when's your new version coming out? I'm interested to see what innovative ideas you come up with this time.