Here is one thing I have found. I am still looking into the SAME issue, and frankly its irritating that it is even an option to mess with aspect ratios. Try this:
In quicktime, under WINDOW/Show Movie Properties
Click on the “Presentation” box and set to Conform Aperture to “Classic”
This will fix it, however I think you have to do it for EACH video. Annoying. If you have found answers since, please send them my way.