@zparegorics No updates available for those themes, unfortunately. When I look for new themes under the Install Themes tab, I find that Twenty Twelve is noted as ‘Installed’, but when I look on the Manage Themes tab, it’s not listed as an available theme.
I am also having a similar issue. I just upgraded to 3.6 the other day, and when I went into my Appearances tab, there was only the currently installed theme listed. There should be far more than that. I even tried deleting a theme from the file system and then uploading it as a ZIP file via the Install Theme tab. The newly installed theme was visible via the initial ‘install successful’ page, but then is not listed on the themes.php page as an available theme, or from them Theme Editor.
They all appeared in 3.5 with zero problems.