I routinely have IR issues with DirecTV , and not just with Harmony. Sometimes placing the emitter well away from where you think it ought to go makes a big difference. I had one recently where I ended up going into Device->Control Devices With->Wireless Extender->Route IR -> IR Blaster just for the DirecTV box. Took care of it. In this particular example the Sat Box was on the floor behind a large armoire, and the extender was mounted high up on the back of the armoire with the 'window' pointed at the ceiling, i.e., the blaster was not anywhere close to pointing directly at the box. I'm probably not spelling armoire correctly, this is a big piece of furniture about 5' wide, 3' deep, and 7' tall, tucked into a corner of a sitting room, with the TV and DVD player inside of it and the rest of the stuff on the floor behind.

Good Luck
Bob