Hi,
I haven’t done an upgrade, but I just installed version 2.3.1. This was giving the same errors from start. So this problem does not only affect updates.
After changing all ID-fields ColinJason said I still had the same problem when I wanted to add tags. I was able to resolve this by also changing the ID-fields of all other tables to ‘auto_increment’ (I guess they should be) and the problem was fixed.
Is this problem known by the developers of WordPress?
Greets,
Jeroen