I skipped the check in counter at AUS, and then my SE status meant nothing to the contract agents at the gate doc checking what seemed like 100 pax. I had to get in the back of the line and wait. They started boarding before finishing the doc check and they sent J pax that hadn't doc checked to the back of the doc check line...so the next time I was at AUS I did the doc check at the check in counter.
That's odd. In the times they haven't paged me, they've always just done it as I've boarded (at other airports--don't think I've been through AUS before). But I try to remember to do it prior to that since it holds up the line by a minute or so.