This was my experience this past week. They scan your right index finger...sometimes. But if the line is long, and/or the finger scanners don't seem to be working right, they use the hand-held scanners on the tickets only.
IME, the finger scanners at US/IOA don't seem to work as well as the ones at Disney. My DD especially had trouble, but they did let her in (eventually) every time. I did see one occasion where a teenager with a ticket printed off the website got an "invalid ticket" message and they sent him to guest services while his family waited on the other side of the turnstiles.