I didn't quite get the bit about IR and RF. Are you using it via RF but when you switch to IR the commands DO work? That is sort of what it sounds like.
Try creating new buttons and learning on them instead. Maybe something flaky has happened to the older buttons. If these new buttons work, you could alias the old buttons to them. Dumb but if it works, it works.
A good answer is easier with a clear question giving the make and model of everything. "The biggest problem in communication is the illusion that it has taken place." -- G. “Bernie” Shaw
