Just chiming in to say I've been experiencing the rescaled parts bug too. It's happening to parts that are NOT the root part, for me specifically with parachutes. For my booster stages, for example, instead of having 30 parachutes, I'd instead set four parachutes scaled to 2x or 2.5x to save on part number count. They show up scaled properly in the VAB, but as soon as I launch, they revert to their original size (visually, at least). I haven't tested to see if it is just a visual reversion, or if the scaled properties are getting reverted too. When I go back to the VAB, the parts are no longer scaled there either, and right clicking on them shows them set to 1x size. There's no errors or warnings in KSP.log when I launch that could indicate what's causing it to happen.