Im not to sure about the problem you are having but the BCM sounds like a good start. I know i had to have mine re-programmed when i installed the factory style driving lights and new switch, it was only like 40 at the dealership.
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99 Z-71 5.3 liter. Jet stage 2, volant cool air intake, flowmaster 40 series, billet grill, clear corners, chrome bed rails, pioneer cd player, Infinity Kappa speakers, silverstars.
http://www.cardomain.com/ride/2094079