I have exactly the same problem, even when i switch back to twentytwelve i get the php warning.
i found out two things while figuring what was going wrong. first, i created a taxonomy-event-categories.php to do som special formating, still either php warning and some formating or no warning but then not formating :(
i followed all advice here, plugins off, switch them, make a lot of extra pages, used all templates in every possible order, still no luck.
i even went to the function in em-category-taxonomy -> function template($template)
and tried die(var_dump($template));
when i get the php warning $template is an empty string, when i get no warning, the template() function never runs
i could give more debug if somebody tells my what to do...