I don't see specific enough information here for me to conclude much.

In any situation with multiple IR emitters, I always wonder about interference. IIUC you have a Pronto emitting both IR and RF and something converting the RF to IR. Depending on where everything is, the device might be getting IR from the Pronto as well as delayed IR from the other path and the two interfere (except when one is so close that it ovewhelms the other). Of course the above descriptions only let me guess at such things. Nothing clearly states that the two paths are are aren't possible in the way this was tested.

As already mentioned in this thread, a sample of Pronto Hex would really help narrow down the possibilities.