Ok, so Above is a screenshot, it is a scorpion based model, facing the viewer. On the left, the scorpions skeleton is linked correctly, however in the physics asset for the same mesh and skeleton, its automatically takes the righthand legs and arm on the scorpion and inverts the constraints, and places the collision as though the constraints were facing properly.
When manually edited the collision can be placed properly, but the translation gizmo for the constraints the second leg joints appear deep inside the main body, and when simulated, this is where the leg bones appear.
In 3ds max, i had mirrored one side to the other, and despite the pivot points being symmetrical, they still show up like this, so im gonna have to assume that was the cause somehow, for it to only be affecting the mirrored limbs.
If and of you wizards out there know the source of my woes, or at least a solution, please let me know, for now i guess im gonna go into 3dsmax and manually replicate the lefthand limbs. Also if there is a better way to mirror bones than just the generic 'mirror' button in the max toolbar, that would be awesome.
Thank you, anybody, for your input.