I got this same error a number of times myself. I knew that I was upgrading correctly, so I couldn’t figure what was going on.
Here’s what I had to do to fix the problem and get everything running correctly. I’m not sure if all steps are necessary (especially the theme part) , but this is what worked for me.
In addition to disabling ALL plugins prior to upgrading, i had to put the theme into default mode.
I also had to make sure that my WPUser had access to ALTER tables in mysql. This was a big part of my problem. After I granted this access, the install went fine.
I then changed the theme back and enabled the plugins.
