Mine had the same symptoms. Occasionally it would work. However, most of the time, when you hit the electric unlock switch, you could hear what sounded like the lock disengaging, but the handle still would not open the tailgate. I eventually found two problems: First, the strikers had to be adjusted down almost a quarter-inch. The latches were tearing up the plastic sleeves on the strikers because they were so high. I THOUGHT that was probably the only problem - but no, the tailgate still refused to open most of the time.
So, I took the latch assembly apart. This is kind of hard to describe, but there are two plates sandwiching another plate that pivots between them on an eccentric path. On my truck the two plates were not parallel - they were pinched too close at one side. So the inner plate would only pivot intermittently. I took a flat blade screwdriver and pried the "pinched" end apart a little. Then I put some more white lithium grease on the plates, buttoned everything up, and it has worked perfectly ever since. The latch is really easy to remove, but takes a little head-scratching to figure out. On your truck, it might be as simple as greasing the two plates to allow the center plate to slide a little better. Might be worth a try while the dealership fumbles around for a warranty solution...
ERIC