You are probably causing a logic loop where PS tries to propagate your operations. Well, whatever, your workflow just sounds wrong. If you need to make transforms, isolate the parts to separate layers and transform the entire layer.
It kind of sounds like a memory or video driver issue. What resolution is your document set at?
Mylenium is correct. When creating frame based animation each frame is linked to a layer. So to animate the motion of the selected portion it needs to be on new layers as it moves (each time you rotate or move, create a new layer. The smaller the increment the more layers needed, but will produce a smoother longer animation). The stationary portion(s) don't need to be on new layers because they are not moving and can be seen due to the transparent areas around the selection.
I hope that makes sense.