Disable the debug console as well

I had a similar issue on two occasions. First time my hard drive failed and I had to get a new one and after I reinstalled everything I stopped getting achievements. The fix I did worked but not sure if it's the only way. I just uninstalled the game, deleted everything in my system for it, reinstalled it and manually copied my save file back in. The weird thing that happened there was some achievements I hadn't gotten because they didn't unlock all unlocked at once.

Then my PC didn't have internet for most of a year and when I finally got internet back and connected steam I wasn't getting achievements unlocked again, but at that point I'd had probably 85% of the game unlocked so I never noticed. Then I ended up transferring my installation from one hard drive to another and copying my save file over which didn't do anything but then I unlocked an achievement which triggered my account to update with everything I'd done over the course of that year and suddenly everything caught up.