Somebody check the (new Beta 4) mass value of the Survey Module. I suspect it's huge, and no longer fits at all in a medium hull.
Hence the autodesigner tries to put a survey module in, fails, and then it fills up the empty capacity with Navigational Sensors instead. Can anybody verify? (Just select your ship, click Details, list all of the components, and manually add up their masses, cross-checking with your own Designer or XML files as needed to get the raw numbers.)