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When you add a splitter bar the front panel it is divided into two panes, and each has it's own origin. You should apply all your desired splitters before you start adding controls etc. because with each split the new panes have their origins reset to their respective top left corners. It's quite useful to have distinct origins per pane as this allows individual control over the contained controls and indicators. It also means that, should you use a moveable splitter bar, then the origin of the panes are moved with the splitter bar and therefore the true coordinates of the items in the panes that get resized are unchanged. This makes it much easier for coding programmatica positional moves.
I fully agree that putting the splitter bars in at the start of a project is the best way, and there has to be origins on both (all) panes but if your updating an existing VI to add functionality it can mess things up big time. it just seemed strange to me that the origin of the 1st pane would get reassigned why not just leave it.