I was having a similar issue...
Trainers wouldn't interact, most merchants wouldn't interact. random items drops and the like, would delve as leather, tho were not equip-able by leather wearing classes.
I Did notice all the mobs effected had been reverted to the default mob brains.. ultimately, I searched, and searched.. and found nothing of relevance.
My resolution for this was rather simple.. I wiped the database... and the server... and everything and started over from scratch.
.. the good ole windows cure all.. format and reinstall! :p