Is anyone else having an issue with the quests not auto tracking?

They took the option to toggle it on/off away.

Ive reset my UI cleared all the folders the Cache/interface/WTF folders

Running no addons.

Any ideas or similar problems?

Not for me :/
I can still toggle quests on and off (assuming you mean the tracker at the very right of your screen)

like, the magnify glass is still there, but everything is checked.

When i get a quest. It doesnt pop up on the right automatically

I have to go into my quest log and click it to quest, its rather annoying