Hello, apologies for the late reply, but I was tinkering around with a few things and sort of found the cause.
The only skeleton affected by the issue is the skeleton I retargeted from for my SMG animations. I mentioned that the retargeted animations only have an issue when my Two Bone IK nodes are connected.
I went into the Two Bone IK nodes and what worked as changing the Joint Target Location Space to Bone Space instead of Component Space and setting the Joint Target to ‘None’. The retargeted animations started animated properly.
However the ADS for the retargeted anims still don’t work, although at least the arms are not ruined although the ADS for all my other anims are now off-centre.
I was wondering if you had any suggestions as to what is happening with that skeleton?