You misunderstand. Of course it square-ifies new shapes. It only scales proportionally after the shape has been created.
Am I going crazy? I'm not holding shift before I press the mouse to make the shape. It turns in to a square when I hit the shift key after I press the mouse button as well. Is that correct as well? My world is falling apart right now.. :S
Any time you hold down the shift key when you are starting to draw a shape or mask with any path tool that is not a pen, the shape will be constrained to a symmetrical form. You can start dragging out your shape and then hold down the shift key or you can drag then press the shape key. Once the shape is drawn then you can grab any corner with the selection tool and change the proportions. Once the shape has changed if you click and drag, any time you hold down the shift key the proportions will then snap back to the changed proportions that existed before you started dragging the edges around. It's always worked that way.
It's not clear but it sounds like after you have changed the proportions of the shape and moved on to another task or tool, if you hold down the shift key the shape returns to it's previous symmetrical (square) form. I've never seen this happen. If that's what is going on then please include your system details, OS version and AE version down to the last decimal point and file a bug.