Focus question

Let's say I set my camera with 70-200 IS II on a tripod (I have a 5DIII, and a 7DII), And I change MA settings until focus is dead on. Now once everything is adjusted, manually move the lens out of focus and then hit my back button focus button. (While still on tripod). I take a picture, and then repeat (manually adjust to oof, hit back button focus and take picture), should I expect every shot to be in focus? Because I am seeing about 1 out of every 4 or 5 shots where focus is missed. This happens with both bodies, and with 2 different lenses. I was also doing this test indoors under normal household lighting conditions. So while it wasn't bright in my house, it wasn't real dark either.

Are you being careful to aim at a contrasty target for the auto focusing procedure? It's important to realize that the camera cannot possibly know what you want to focus on all by itself. I leave my 7D set for center focus point only and make sure the target it's aimed at is not only at the distance that I want my focus set for but also that the target is something that the camera can reliably use for autofocus. If this cannot be done, I'll typically use manual focus.