linkman2004 - Okay I found a work around. I added an action which repositions the bones. If you call the action just before using 'set position' etc everything should work fine
I also made a modification. When the mouse is over a handle or a point, it becomes a bluish colour. This makes it a LOT easier to work out what limb will be affected if you start dragging. Its quite amazing how a bit of highlighting can really help out in confusing situations!
Oh also, always setting an animation no longer buggers up