Go to the My Documents\Elder Scrolls Online folder and rename the Live folder then launch the game. (don't delete it as you will lose all your UI Mods and related settings)
This will reset the game to defaults but doesn't require redownloading a patch. Load the game, reset your graphics/controls the way you want them and check to see if the Ghosts/Projections are visible now.
I was able to do the Fort Virak Quest after doing this since I could see the ghosts in order to avoid them.
I put my AddOn and Saved Variables from the renamed folder back into my new one and I can still see the ghosts etc.