I had the same problem with my RFX9600 and it took me a bit to figure it out.
In PEP for some reason some of the devices such as the amp,sky and dvd player
had doubled up in the component list and the ones that had doubled up the extender box was not ticked.

As soon as I ticked them and downloaded to the remote all worked fine.
This took many hours to work out and I do not know why it doubled up on some
components and not others,something to do with Windows 7 64 bit maybe.