I've never had this issue myself (except when reflashing a tune using HP Tuners, but deleting the code is all it takes).
There's a TSB on replacing the throttle body pigtail, which I think is where the problem lies. I believe the wires start breaking down, even though they look fine on the insulation or something like that.
What I've recommended to folks on the forums is, finding a wiring diagram, and backprobing the throttle body and the corresponding wires at the ECU, then running jumper test cables temporarily. The temporary leads will prevent signal loss between those two parts, because you've provided an alternate electrical path.
Drive it around and if the problem is resolved you know where the problem is. You can either replace the pigtail and hopefully the wiring issue is there, or simply run a new set of wires, with wire loom, you probably won't even know it.