I might be Grey Goo... As a test, I loaded the game, got automation, saved, loaded, saw it was reset, then quit to tinker with my mod list. I removed grey goo, loaded the game, and my research progress was BACK! I had automation again(but not my prior lost techs, probably cause I saved with JUST tha...

I'm also having the same problem, here's my save. Hopefully this works.