I've found that this happens in one specific scenario: when you are connecting to AccessPoint via QlikView Desktop and you clone an existing object (one built into the qvw).
When you clone the object it will create the new object 10 pixels to the right and 10 pixels down from the original object. If you then move the new cloned object (either by dragging it or adjusting the object coordinates) it will appear to move OK, but when you close your session and re-open it the object will revert back to the original position (10 pixels away from the original).
So the solution is to not clone objects when connected to AccessPoint. Just copy and paste them. You can copy any existing cloned objects and then delete the cloned object to fix any outstanding problems.