It's very hard to understand correctly the issue without a screen shot :D
Anyway i guesses i can understand what you mean. For the newest version maybe i did adjust the default camera focal length.
So it makes the object look like being stretched in the z axis? Is it what you tried to describe?
If you have the Pro version, you will be able to adjust the camera focal length in the Trinus tab i remember correctly.
I wish i had nvidia 3d vision or 3d tv ... Lucky guys!