Hi, I have a series of WP blogs installed in a subfolder (not the root directory) and the latest version that will work on those is 3.4.6 (and it works perfectly). I've been able to install newer versions until 3.5.3 correctly on the same server and a similar set-up _but with WP in the root directory_ on another site.

Need more info. I have several sites in sub folders ie mydomain.com points to root while mydomain2.com points to root/site2

Do the sites work if you are using the twenty-ten theme?
What version of wp?
What is a URL of one not working?
Does the backend work?
What happens ..what does the site look like...what do you mean by it doesn't work?

Hi!
The blogs are on a url like this: root/blogs/nameofblog
Atahualpa is in the right folder and works until version 3.4.6

I have the latest WP version (3.0.1)
Twenty-ten does work on the same blogs
The backend works

Because this is an official municipal site whose blogs are presently not publicised, I'd rather not give the URL publicly if I can do without it but I can tell you the only thing I see on the front-end is this:

"Powered by WordPress & the Atahualpa Theme by BytesForAll. Discuss on our WP Forum"
with Wordpress, Atahualpa Theme and BytesForAll being links.

That's it. The rest is a blank white page.

In short: 3.4.6 works perfectly. Anything beyond doesn't. I have 15 blogs installed like that and the problem is on all of them.
I have other blogs installed on the same server/hosting/setup where the WP installation is in the root and those work fine with 3.4.9 and up.

On info that might help: In the root (public_html) I have a Joomla install.

Ahh go to the export/import settings page and press the 'delete bfa_ata4' button and see what it looks like.

Starting in 3.4.7 I think it was, atahualpa starts saving the database options in one row of the database to reduce database calls. It may be that the build of the one row got messed up (it has happened a lot) so this will delete the row and rebuild it from your 3.4.6 settings. Once it works, if you make more changes, do not delete it again or you will revert to your 3.4.6 settings again