I'm not sure what happened, but when I updated from 3.7.10 to 3.7.12 theme Theme options page is totally borked and most confusing to read, nevermind actually do anything.

I've uploaded an image to illustrate an example.

Try resetting your permalinks

Got the same problem as shown on screenschot supplied by initial poster. Tried all the solutions you suggested (permalink and plug-ins off) No success. Tried installing Atahualpa 3.7.13, header totally lost! Tried installing Atahualpa 3.7.12, same messed up ATO page.

I'm now on Atahualpa 3.7.9. Should I update first to 10, then 11 then 12? If yes, where do I download these earlier Atahualpa files?

Is this a bug? If so, please point me to the fix!

Thanks in advance!

At this point you can just go to to 3.7.13. Then click the save on the header and footer areas which should fix the header and footer not showing issue. Then see how things are.

I also get the same ATO page (as in the screen shot provided above) when I upgraded to 3.7.13 so I rolled it back to 3.7.9. I'm nervous that if I click save on anything, I would not be able to roll back to the old one if things don't work out right. Is this fear grounded? Can I roll back to the old version anytime?

Why is this update bugging? Previous updates didn't cause so much headache.

Thanks for the response, Miles.

I never roll back to earlier versions. I don't think clicking the save button will do anything to prevent you from reverting to an earlier version but since I have never done it I can't say with absolute certainty.

The best insurance to let you move back is a complete backup with a tool like BackupBuddy.