Ah, I understand what you mean now, the scene root has changed its orientation and is "dragging" your model across the wrong axis. This could have something to do with the way you are animating, I suggest moving the scene root a bit forward each time when you do each keyframe. I know autokey can do this automatically but as you said when this happens you get red keys and I think this could be your problem. Failing that just move the root bone along the negative x axis and hopefully it will rotate it onto the y ;)