Toggling setup mode on and off causes multiplied mesh movement each time for some joints(particularly head/neck joints). Each toggle causes the effect to double, making the mesh rigging more and more offset each time and making it difficult to work on painting weights.
Heres how it looks after toggling setup mode 10 times:

I can temporarily fix this by doing the following:
1) Toggle setup mode off
2) Switch modes (vertex/edge/poly/SEL)
But toggling setup mode repeatedly will cause it to start again.