I have tried to googling and searching a lot about the subject, nearly though I had found the solution, but... still not really. Most of topics about multisite and themes are about other stuff (default theme for new sites, or things like that). Don't fit to my problem. Sorry if somehow I missed right post. Ok, let's go...
I have a WP 3.5 multisite installed and bunch of sites declared. Another bunch of themes, some plugins and so on. Everything was working perfect. On primary site I had selected theme - let's call it CURSED theme :)
One day I was changing primary site's theme and it went well, apart of opening my site in different browser (within being not logged in as any user of my network) and bam! - I've seen different theme that I've selected.
From that point the CURSED theme was all the time selected in Dashboard->Appearence no matter that I tried to change it for a different one. If I deleted a directory - it was still selected as current theme, of course not available but selected still. If I selected another one - no changes in Dashboard but... somethimes non logged user could see it properly while visiting the site.
Going to SuperAdmin network settings, disable theme for network and enable it in Site->Edit panel works fine, but... show it only for logged user while visiting site.
I checked wp-config.php - there is no wp_default_theme declared. Also checked for wp-includes/default-constants.php - everything's looking normal.
I went to SuperAdmin->Network->Site->Edit->Settings and found the entry Default Theme with “Twenty Tvelve” declared. Deleting it (setting to empty field) does not change anything.
My latest state is - I can change theme visible for Admin in SuperAdmin->Network->Site->Edit tab, of course for theme that is not activated for whole network. I can also change theme visible for non logged user by changing in Dashboard->Appearance but it still does NOT show it was changed! Constantly showing SuperAdmin theme as selected, but displaying it for visitors.
Eventually I can manage themes in that weird way, but not getting to set very same theme for all by one click and seeing change confirmed - just as it supposed to be.
Please, does anyone have any suggestions how to solve the problem?
Ps. Can it be anyway related that before that weird behaviour I installed and unistalled wp-ecommerce? Day or two before, and that I realised things are getting messy.