I've had horrible problems with this upgrade also despite following instructions. I've been using WordPress for a bunch of sites and for a long time and have upgraded MANY times. I have never had a single issue. This has been a mess this time.
The Admin doesn't work at all - as in, when you save anything the admin disappears - entirely. I have to type in the URL to the Admin to get it back. Changes are not reflected in the Admin but show on the site. If I navigate to another area of the admin and come back to where I had been making changes, the changes magically appear.
I also had my entire site disappear - the database suddenly could not be found after I had attempted to add a widget to a sidebar that was working perfectly before the upgrade. It was just a standard widget, not a plugin or anything - yikes!
I've been all over the codex looking to see if I missed something but there's no help. I'm sure there's a line of code that needs to be somewhere to make this thing happy but I have no idea what that might be.
I did get the site to find it's database and it's visually OK but trying to add or edit content is a complete nightmare.
I attempted to roll back to 2.6.5 but that didn't work either. I'm thinking of making another attempt at that and see if I can get this thing to be useable.
AND, yes, it is a mess no matter what theme I'm using and regardless of plugins. It had occured to me that it was some weird thing in a plugin or in a custom theme. I've had an entire festival of troubleshooting and am no better off than when I started.
If anyone has any clue as to what might make the admin and database hate each other so much I'd be very appreciative of a push in a right direction toward making them happy again. I do love WordPress and am shocked at this behavior ;-)