Unfortunately switching the parent bone just made it worse. I tried to adjust the transform constraint because the parent bone change and it just ended up moving the bone in setup mode even though the leg IK wasn't moving at all. I made sure to click the match button before I made any changes too.
I tried to replicate what I did on the left side to the right knee and it had the same issue of the bones moving/scaling in setup mode when nothing else was moving. I made sure to "match" the bones every time, deleted the constraint and recreated it several times.
The back of the Knee IK also just moves really fast/ collides with the rotation bone when I attempt to recreate it on the second leg. I'm not even sure what I did to get the first IK bone not to move as much. That IK Mix influence was still at 100%.
I'm not sure if its just a bug with the new beta but I don't think this happened with the stable ver of Spine. Unfortunately I can't downgrade my file since I already saved in the latest beta yesterday.
Thank you for replying so fast!