I know this probably sounds very odd, but do you have any devices plugged into power/USB ports in your truck? Try unplugging all of them if you have any.
I had the strangest behavior with my truck remote. It would only work close to the truck, and very sporadically. I replaced the batteries in the remote. I tried using the 2nd 'spare' remote. Still had the same behavior. By chance I removed my old Creative Zen MP3 device one day, and the remote worked fine. I never traced down why the Zen was causing a problem. However I was able to reproduce the problem by plugging it back in to the power port.