I restored a "temp music" partition onto a new disk (partition) so I have X3d running on my "main" music partition and X3c running on the temp one. I have various backup images so I restored to X3b and then upgraded to X3c.
I don't have any Waves plugins Conley - but I'm having the same "can't save settings" (which really has nothing to do with presets) as you are - AND it works fine (with the VST3 version anyway) in X3b and X3c - but can't retain settings in X3d. That's the only reason I'm here - to see if you get any ideas of how to fix this, and hope they help me too.
Oh - and to remind Alex that I've reset
AND rescanned