This seems like a bug to me, but perhaps I just don't understand UV unwrapping enough. I am using Blender 2.59 from blender.org.
I started with the default cube, scaled it, Z axis by 0.125, then I cut out a hole in the middle, essentially turning it into a rectangular torus. I marked some seams, UV unwrapped, and did not get anything unexpected. Here is a screen capture.
It was what I did next that threw me. While in edit mode, with all vertices selected, I scaled it, Y axis, by 4. Then when I UV unwrapped, it came out distorted. Here is a screen capture.