"burnt out" window/lock switches and burned harness

[Real Fast Bug]

So my truck has been at the dealer for like 3 days now. Took it to have them replace both driver and passenger side power window/lock switches under my extended warranty. The power locks stopped working several months ago from the inside switches. However, they still automatically lock when you start driving and also work if you lock the door with the key they both go down. Also with the aftermarket alarm remote only the passenger lock goes down. Then over the past few weeks I noticed that the passenger window intermitently would not work from the driver side but could usually get it back up on the passenger side.

So the dealer got new switches and said within 10 minutes of installing them the passenger one started to smoke. Also while in the door (passenger side I believe) to install them they found like 3 inches of wiring harness "burned up" and repaired it. They think there is a short but can't find it. The frustrating part to all of this is that I am very able to trouble shoot this stuff myself but went into it thinking the switches had flaked out and figured my extended warranty would be happy to replace them for me....... Any way now its friday and no truck. Any suggestions on what may be shorting out these wires? From my service manual it appears the windows and doors do not share any circuits and that the only thing they have in common is their close proximity to each other. Only other idea I could come up with is maybe they pinched something when they replaced most all of my A/C under warranty last year.... theres a whole other story... Thanks
RFB