I just went on a trip from ORK-LHR-SFO. I checked in 24 hours before the LHR-SFO leg and got both boarding passes, and went off on my ORK-LHR flight. All well and good, except when I went to board in LHR, the machine went beep. For the briefest of seconds, I was hopeful of an op-up, but it turns out I'd been marked as a misconnect, despite having an assigned seat (which I'd paid for) and a boarding pass.

The guy there pressed a few buttons, called someone somewhere and I was free to board. Since I was by now the very last to board, I didn't have time to sit around and talk to him about why this was or what I'd done, and had to run aboard, but can anyone here tell me what could have happened. I would've suspected a cockup in ORK, but I checked in online, so I just don't know.

Did you have a single ticket from ORK on a codeshare? And how long was the layover in LHR?

The only thing I could think of is that you may have had to provide some kind of additional information at checkin (as happened to us recently on a trip via MUC) which they hadn't gathered, so they marked you that way?

The only thing that might have happened at ORK was that somebody didn't bother to do whatever they needed to do to make you "checked in" and decided "It'll be grand, so". And just let you board anyway, so that you showed up as not on the flight when you got to London. I could actually see that happening.

It's a total guess, but if it was all one ticket on one airline, I would guess that somehow they thought you missed the first segment. Because you were standing there they realized the system was probably wrong and banged at the keyboard to get you on the flight.

2 boarding passes, both were marked BA, but the ORK-LHR was a codeshare flown by Aer Lingus. It just seemed odd, and like I said, when the beep occurred, I thought it was op-up, to go from there to 'uh, the computer says no' was a bit disappointing

That's likely why. I don't have experience with BA/Aer Lingus, but I fly UA/LH a fair amount, usually beginning with UA at ORD, and LH always wants to reprint my boarding pass before boarding my continuing flight. Now I just proactively go to the GA to have it reprinted. I'm not 100% sure that getting your BP from another airlines means that it actually checked you in on the other airline's system.

Could've been a passport/visa note to the GA. I don't know if BA has a pre-fill but on AF and DL that is sometimes the notation given on the reader.

I'm going to guess that Air Lingus didn't properly report you as being on the flight and your ticket got zapped.

Were you on BA from LHR-SFO? If so, did you have any trouble at the boarding pass check before security at LHR T5? In either case, did you use the proper back steps bus to transfer at LHR?