I don't have any experience with dual/aux tanks, but others have written about problems with the gauge reading zero when the aux tank continually feeds into the main tank. As I understand it, the truck computer has a sanity check and sees that you've driven some number of miles without using any fuel since the main tank stays full. That can't be, so it decides there's something wrong and sets the gauge to empty.
One solution would be to close the line when you're driving, and let the aux fill the main tank when you're sitting. Or maybe you wait until the main tank gets low, open the aux, know that the gauge might say empty at some point, then close the aux later.