2006 dodge ram wc1000 window module

Alright I put auto loc wc1000 one touch window modules on a 2006 Dodge Ram. Here is the fun part, went to the door and made the connections at the master switch for the driver and passenger door. Wires soldered life is good. Went straight to the battery for power for the units hooked everything up got a good chassis ground, used relays hooked the up function to lock and the down to aux 2. The unit works great via the remote and the driver factory switches work like a champ until I crank the truck up then the windows will not roll up or down, all the way just in incriments. Here is the cool part that only happens with the factory switches I can still operate them with the remote and they work like they are supposed to.     I went back to the switch and checked and what I am thinking is that for some reason when you crank the truck up the motors do not rest at ground. Directechs does not say a thing about this but I called tech at Stinger and they said in their database they have a note that the motors may not rest a ground. Any suggestions?

Not a bad idea I will give that a try. I swear these Dodge and Chryslers are starting to give me a complex.