sounds like its picking up noise from the pulsing from the traction and pump motors but i dont see how the keytroller could make the truck lower, all it does is turn the truck on and off and monitor impacts if it has that option installed.
Have you tried relocating the connections where its connected to it's power sources? Also what stam suggested is usually imperative when installing shockwatches or keytroller devices, they even usually recommend it. An inline power filter should eliminate any noise the system generates and translate the 'dirty power' from the battery into a stable energy flow.

One other thing is check where the cables are ran, if they are near any motors you will probably have to re-run the cables away from any motors or use shielded cable or something.

just some thoughts about this strange issue ;o)