Yes they do actually. I turned in my transcript and had my app filled out two weeks ago and they actually verified my transcript and sent it back due to a problem. this was two weeks after they marked it as received so it seemed like they were verifying it and that it was what the email said. I think people who were processed within an hour of submitting had their stuff verified before because you can see they all had their transcripts in really early like me.
Edit: But this is probably only true for people who had stuff in really early, not now when the number of apps increases and they start to back up.