No sure what happened but updating to Joomla 3.3.3 solve it: I could reproduce under J3.3.3, the same error I had under J3.3.1 by modifying the module chrome file (\templates\mytemplate\html\module.php).
I haven't edited this file since a least a full month before the issue happened so I can't find out what was wrong.
Anyway, it's back now!
EDIT:
Actualy updating to 3.3.2 didn't solve it, but it helped me to find a way to go around the bug. For still unknow reason, if I have a modules.php in mytemplate/html, then some pages on my website are unavailable. I went around by adding my chrome directly in templates\system\html\modules.php. Not the best method but at least my website is back and with a nice module chrome!