After a long search I finally found why my template styles suddenly stopped working: the Hikashop affiliate plugin stop it from functioning.
Replicate:
Basic J2.5 site
Duplicate the Beez2 template style and call it green, set the style to green too.
Assign it to a menu item.
In the frontend, select that menu item and see, depending if the plugin is enable or not, the style switching or not.
With the plugin enabled you will only be able to see the standard / default template /style.
I have tested this with several templates and all have the same error.
Happens on Apache and IIS8 sites.
If needed I have test sites for replication ready and will leave them for a few days.
Bastiaan Houtkooper
Zebra Hosting