I wouldn't worry at all.
1) Your warranty protects you for a lot more time.
2) What everyone said about it being a complex issue to diagnose the problem is true.
I have a few guesses myself to what it could be (sounds like you are losing spark in a cylinder, I'd guess a coil pack or something in the ignition is at least part of the problem), but the bottom line is that, though it's a hassle to have to deal with, you should be fine. Worst case you may have to take it back once or twice to get it nailed down 100%, but I'm guessing even that is a stretch.
