1. All RF is suceptible to EMF, so you want to ensure that the receiving unit is placed, or has an antenna that is placed, away from EMF generating gear, most notably DVD players and DVRs with spinning discs and magnetic fields. The top of the rack, or on top of a shelf or just a foot or so away from the rack can do it.
2. IR is more reliable when using an IR emitter with RF... most of the time. This is very much a question mark and helps a fair bit when you choose the right gear. Panasonic and Sony are WAY up on the list of manufacturers who really have it figured out. Philips (the make of the Pronto!) is one that I put near the bottom of the list.
3. Look for discrete codes at Remote Central - Discretes are what is is all about, and buying the right product can really come into play here. Most major brand receivers cover this, but Yamaha and Denon are simply killer when it comes to this.
I've used many Crestron systems which all utlize RF, and have had mixed results when the antenna is to close to the rack, but near 100% reliability when I've moved the antenna outside of the rack. In my home, I get 100% hits from 50+ feet away from my master bedroom to the basement. I would bet I could walk half a block away and still control the system.