I assume you must be using the run-time movable controls instrument driver tool since it sounds like you are moving/sizing controls at runtime. The SavePanelState/RecallPanelState functions weren't designed to take into account design-time changes like movement of controls. Unfortunately, there isn't a way to do what you need built-in. What you would have to do is write your own data file to save off the position and sizes of the controls (using GetCtrlAttribute to get the sizes/positions) and read that in and reset all of the controls based on the sizes and positions in the file.
Best Regards,
Chris Matthews
National Instruments