My vote goes to bad form.
Excellent form is crucial for squatting because (a) it makes the lift easier, at least that's what I've found, and (b) it's safer. Here's a couple links to sites with good squatting info:
VERY detailed explanation of proper squat form
Mike Robertson - 10 Tips for Flawless Squattin'
Some good squatting pictures
From what you said, I'd guess that you're doing 1 or both of the following:
1. Not keeping your core (including your back) tight throughout the lift.
2. Allowing your lower back to round at the bottom (picture 3 in the last link), and as a possible result of this you straighten out your legs but the bar doesn't move so you end up having to "rounded-back good-morning" it up the rest of the way. I know I've done this in the past, and it's definitely not good.
My advice is to
really work on good form, especially keeping your back tight and arched throughout the entire lift and keeping your chest up. I can't stress the importance of good form enough. Work on it now to make sure you don't have injuries later.
Full squats shouldn't hurt your back if you keep your back properly arched the entire time. Also, just my opinion here, but unless you're super flexible there really isn't that much difference between a full squat and a parallel squat, where parallell squat is referring to the line connecting the knee to the top of the hip being parallel to the floor (picture 1 in the last link).
If you're looking for an excellent source of information on proper squat form, check out Mark Rippetoe's "Starting Strength."