I had the same problem.
My Bravia LCD TV wasn't responding to its remote RMF-GD001 although the remote works on the home entertainment unit. Lucky for me, I have an extended warranty and so I called for a service. Technician tested my remote and said that it's RF transmitter is spoilt. Little did I know that the remote has IR and RF transmitter and it will work on any devices that uses infra red transmission. But Bravia LCD TVs use the radio frequency transmission and that is where the problem is.
I had my $125 remote replaced FOC.
This reminds me to get a silicon case for the remote and to put it out of reach from my kids who like to drop things.