I installed my delete, MM3 programmer, and I'm having some weird issues... not sure if they are related or not.

When I start my truck, it almost stutters to start as if I have a dying battery or failing starter.... it has never not started yet. Then when the truck is on, the MM3 tuner flashes red red green red red. I have to unplug the USB cable from the programmer and the CANBUS cable, wait 10 seconds or so and plug them back in to fix the problem EVERY TIME I start the truck.

Anyone have any ideas for something I can look at or perhaps this is a common issue if people do X wrong, or whatever? Thanks for input in advance