Ok so I have great news, this should be a definitive answer for many questions.
I have a Kuro 111FD which has an IR Repeater Out, SR Control Out, and of course through the HDMI CEC the Kuro Link controls.
I have an SC-77, BDP-23FD, an Apple TV (not the new CEC one) and the black Dish VIP211k in the cabinet.
I have this IR Repeater also which is dual band and so, when the emitter is positioned absolutely perfectly down to the nanometer, works even with the dish receiver (it's one of the few that does) http://www.amazon.com/gp/product/B00...ilpage_o00_s00
I use the KURO remote since it has the nice red LED feedback on the bottom.
I have the SR Control Out going to the BDP and that has always worked fine.
KURO Link works fine except that it always switches the receiver to optical in when they turn on together because of ARC. Nothing I can do about that except manually switch the input afterwards.
The IR was interesting, and confusing. I had your problem. Anything but the dish VIP worked when the 3rd party IR setup had an emitter in front of it, whether the signal being emitted originated from the TV or 3rd party IR receiver. Also, everything but the dish receiver worked when those emitters were only emitting the IR repeater passed through to them from the IR out on my SC77. But I couldn't get the SC77 itself to respond to any IR command except that coming in the receptor in the front of it (via a 3rd party IR emitter or the remote directly). The infrared from the TV and Repeater going into 1 and 2 IR ins on the SC77, and the IR out on the SC77 was going into the IR box as an extra IR receiver. So while components responded to the IR when the emitter was in front of the respective device's receiver (the Apple TV and the Dish box), where the receiver is passing the IR through, the SC77 wouldn't respond to IR commands. It was weird that it would receive the commands and pass them through, but not respond. It doesn't have an SR Control in, and the volume is adjusted quicker using IR than KURO Link which adjusts a half decibel every two seconds, so I had to ether stick the emitter in front of it or figure out how to get the built in to work.
I have the cable from the TV IR Repeater Out going into IR input 1 now, no other IR cable going into the receiver's other IR in, and nothing coming out of the receiver's IR out. IT WORKS
That means that either it's because the Pioneer TV is the exclusive sender and their IR repeating is somehow different, or because when you are using IR Out on the receiver it does not absorb the commands itself.
Hope that helps, and if anyone wants me to try a configuration to figure it out more I'll give it a shot.