Today I manually updates to 3.7.1 (from 3.6.4). The site works, but there are several problems.
First of all, the theme options are all shown on a long page with no styling. Could it be a problem related to caching (I'm using w3tc)?
Then, my page menu, visible on www.fotocomefare.com, after the update includes some pages which are not specified in the menu.
Finally, to questions.
First, using manual update, which settings are moved to the new installation? Which ones need to be copied?
Second, php. From what I understood, php is no more allowed in any text box in Atahualpa options. Am I right?

For the menu issue - when you are using WordPress custom menus and then change theme you need to re-save the menu in the Wordpress Admin Menu -> Appearance -> Menus -> Theme Locations Section of the options.

Originally Posted by GarethP

For the menu issue - when you are using WordPress custom menus and then change theme you need to re-save the menu in the Wordpress Admin Menu -> Appearance -> Menus -> Theme Locations Section of the options.

Thank you, will try it.

All theme options are stored in the database
No php is allowed with the exception of the syntax for new widget areas since the theme parses them

Originally Posted by juggledad

All theme options are stored in the database
No php is allowed with the exception of the syntax for new widget areas since the theme parses them

So, even if I follow the manual procedure and upload the theme in a new folder, when I activate it, it should load options from the database?

And about the options shown altogether on the same page?

That's right, the new version will read the options from the database and they will show in the theme option pages.