Hi
That seems to be the way QuickTime Player works – its for playing movies on a computer desktop and has always only understood square pixels.
Once you have finished editing in a non-square-pixel savvy application like FCP/AE etc and exported a final version then you can use QT Player Pro to resize the play window to give the correct aspect ratio, and Save the movie so it remains this way. To do the resizing, open the Get Movie Properties window, select Video track on the left, and Size on the right, which will show the pixel size of the QT movie.
Then hold down the Shift key, and resize the player window until it is altered to 640×480 (or whatever you need to give it the correct the aspect ratio).
Then Save the movie to make it stick this way when opened in all QT-playing applications.