Only thing I can think of is either there is something screwy going on with the wiring that with the lights on the singals are getting crossed somewhere or your battery is going. Too much strain on a battery can make some things work and others not.
Gotta look at it as your battery being an over worked guy trying to multi task. If you have a good ammount of aftermarket stereo equipment as well as the lights going and what ever else electronic wise youve got pumping chances are it just doesnt have the power captain.
Invest in a racing spec grounding kit. You can pick one up on ebay for like $30 TRD shipped or $50 GReddy shipped.
It wont do like it claims and give you any hp or torque but it will help out the battery with all your electronics and help boost your tuner strength. Ever since I put mine on I can pick up my techno station in the boonies.
