Andrew, your roto-ing technique is wrong. If you run with only the tips of your toes or will only the balls of your feet touching the ground, it doesn't matter if you run for 10 meters or a marathon - in a stadium or across the Sahara - it's still wrong.
I've never seen nor heard of such an issue as you are experiencing but I am pretty certain that your issue is related with your roto-ing technique.
You now have a keyframe on each frame; unless you have interlaced footage within a suitably designated comp, there will be no interpolation from one frame to the next! This is basic animation or keyframing logic.
I have a wee bit of time to look at your issue if you can post the clip and the AEP on the COW for me to have a look-see. In fact, I doubt if I need the clip; just the AEP will do.
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