I can't seem to get rid of this issue either, I replaced the alternator twice, and ended up returning them both and going back to my original because the issue stayed the same. I even ran with the fuse pulled like this thread suggests, with no change (it still locks/unlocks). The transmission has been rebuilt, TC replaced, I've wrapped wires near the alternator with tin foil and duct tape, I even put a small capacitor in between the tranny line and ground to try to smooth the current (and later removed it, since it had no effect either).
The APPs is pretty new too, since I replaced it when I first bought the truck (dead pedal).
I'm completely out of ideas, what else can I do?