Not actually. if the NGO is currently not in compliance or were found not to be a true NGO, then that's the issue which it sounds as if it is. It may be a rule change (doubt it) but even if it is then the NGO isnt compliant and it doesnt matter what past rules were in place, you play the game with rules currently in force. My assertion is your speculating and claiming foul play without any facts other than the NGO is having issues. Contact the NGO and ask them why they are no longer accepted as an NGO for volunteer visa status in Thailand.