I'm having the exact same issue, even when I set the plugins text file to read only, later it just gets set back. I've done everything OP has done. The funny thing is if I look at NMM and enable everything, check the plugins txt file, its all fine. Then if I watch the plugins in the NMM.... after a few minutes I see them all get turned off (un ticked) and checking the plugins txt file its normal again. I'm just like, why the hell is this happening.. ;-;