My theme is automatically disabled!
Do you mean you have 2 URL (www.ex.com and sub.ex.com) with the dir/ and files:


/sites

   all/

      themes/

      modules/ 

   www.ex.com/

      themes/

        your_theme/

   sub.ex.com/



and no "/sites/sites.php" in here? (read for ex "example.sites.php")

And selected in www.ex.com/admin/appearance for ex bartik as default
and for sub.ex.com/admin/appearance "the your_theme" as default (and clear cache)?

and each time, you need to go in sub.ex.com/admin/appearance in order to set "the your_theme" as default, with no error in logs?