So, I tried RMIR instead of Remote Master and that has made a huge difference. I changed the protocol for FLIRC to NEC2 and reprogrammed the FLIRC. Now it's working great. Now I just need to program the remote to shut everything down when I hit the power button and it should be good to go. But really, RMIR is laid out very well and a good piece of software.

Are there going to be any plans for custom icon support for the Favorites?

Thanks for the assistance.