Updated to 10.1 and now all tracks with Soundtoys plugins loaded back with default settings instead of however I had them set and I have legit plugin license.

Any ideas what gives?

 

Maybe try to save the preset first in Soutoys on each track you are using it.
Try simply on a new project with 2 or 3 tracks with sountoys, maybe with some automation, save the preset in Soundoys give it a name and then save youre Ableton project. See if the same presets are available when reopen Ableton.
Otherwise I have no idea.