Hi, I just had the belts replaced on my 03 Neon as per a recommendation from Pep Boys. Nothing seemed wrong with the old ones, but I went ahead with the change. Everything seemed fine for the first couple days, but now when I start the car up, I hear a squeal for the first couple seconds and then it disappears. It only seems to happen from a cold start if the car has been off for a few hours. I called Pep Boys and they said the Neon had an auto-tensioner, so that wasn't the problem, but I couldn't get it in to them today. Anyone have any ideas? Does it just need to be tightened, or Wd-40'd? Will it go away once its worn in?

That is the classic noise of an alternator belt that isnt quite tight enough. My Neon is a 97, and it doesnt have an auto-tensioner. I have had to tighten the belt after the first few hundred miles, and again a month or two later. No more squeals.
If it has a tensioner that is automatic, it could be the tensioner is faulty, and either doesnt move smoothly, or has a bad bearing in the pulley. Im fond of replacing the tensioner pulley (and idler pulley if it has one) each time I replace serpentinve belts.