I tried reinstalling also. Didn’t help here either.
I tested a few other theme’s they all seem to work with the customizer (but they do have other settings and customization). The ones I tried had updates available right after WordPress updated this morning.
My lesson learned, WordPress automatic update is not something I really want, I always wait to update anything. I had automatic updates disabled on my plugins and theme, but not WordPress itself, didn’t even thought about that. I’m used getting a notification that an update is available on other software I use, not used to auto update things, especially a server.