It’s strange that as I look for a solution I just see how others have this problem as well.
That thread is helpful but I don’t like that the solution so far is to just disable IK, especially in our cases with ground based animations. Not much of a solution to just get rid of it.
Reading down to the bottom of the thread however did lead me to find that the IK bones are in fact not animating for some reason despite me adding keys in the control rig before baking.
So I don’t know why its not applying the animation to the ik bones but this seems to be the problem.