Probably the wiring harness is different and it might be trying to pull power from something it shouldn't. I would trace all the wiring and see where it goes and find out where you are pulling power and ground from. Any other electronics working funny in the truck?
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06 Mega 2500 4x4, G56, 12" custom lift, bodyguard front and rear bumpers, 20" Novakanes with 41" Michelin XL's, AFE Mega Cannon, Smarty S-06 POD, Edge CTS Insight monitoring, 5" Flo Pro exhaust, and CFM+ Intake manifold.