Always happens on the first save of a new game.
Loading and saving over it usually fixes that particular message.
The script that handles the Previous Version Save support only seems to trigger on loading a save, hence the prompt.
Extract this into ModScripts, overwriting when prompted. It'll now silently do its thing, but should still get logged in the debug console.
Note: just changed the msgbox statements to prp statements, while adjusting any if statements that potentially could of not worked as expected.
EDIT: Redone version that outputs to the debug console via
prp