530t window module issue Chevy Silverado

I have a Viper 791XV in my 2003 Silverado truck.  I was preparing to install the 530t window module and am having some issues. 

After wiring the drivers door according to the instructions regarding vehicles with a factory control module, directly at the motor, the window works fine with the alarm remote disarm and roll down function. The window switch in the door is completely eratic now though.  It only goes all the way up or down, sort of like the one touch function with no stopping or modulating in between.

Is there something I should know about this application?

Thanks,

Is that setup my only option with this application?

Actually....the windows do not stop after trying what you suggested.  They merely pause and continue on in the direction they were headed.  Basically they cannot be controlled, and they will occasionally go in the opposite direction expected.

Could I be experiencing something else?