You have now clarified your with the info that the Dish Hopper is RF only. Reading back with this info in mind now, it makes sense. I also read my first reply and realized I left out a part as well. I started to ask if you pointed the hopper remote at the equipment, and not just your repeater system, but someone jumbled that question into the next, where I meant to ask if you programmed the 780 and with IR or RF only. So I think we both sorta confused the other.

The answer to your last predicament, getting two hoppers to work in the same room. If you did or do get IR to work, the easiest and most obvious answer would be to swap your ir repeater for an rf kit. You could then assign the emitter ports allowing for separate control of the two hoppers.