I think I'm having the same problem.
In my case it seems like there's no problem selecting faces on the sides of the model, but when I try to select a face that lies on the top, then the faces on top acts as if it wasn't there and a face underneath it is the one that actually gets selected.
If you picture a box, I go to select the top face, but SU actually selects either the bottom or one of the sides.
Weird...
No problem selecting faces.
Behavior seems to stop when using X-ray (ie. selection works like it should).
I tried ticking and unticking boxes in the preferences but that didn't work.
UPDATE: Tried once more turning off hardware acceleration and problem seems solved.