i am not sure but i know rigging can be a pain in the (dark hole where the sun never shines).
i think that it has something to do with the ik handles and constraints you turned off if you move joints individually when you turn of constraints/Ik handles it can give strange results because once you turn it on the joints get affected by them again.
my advice to you is first set up your rig as completely as possible (ik/fk blending constraints etc and at the very last start binding