AS' physical check-in is usually a nightmare (especially at SEA), which is why the kiosks are so critical (they make it a breeze). I don't fly AS anymore (nothing to do with the airline - great people and service), but when I did, I was always aghast at how bad the physical check-in lines at SEA and LAX and SAN were - even with all stations manned. It truly amazes me how few of AS' pax use their electronic check-in, but I think so many on the SEA/PDX-SFO/LAX routes are leisure folks going to and from Mexico or the southern CA theme parks who only take one or two trips a year.
True, if you had arrived 90 minutes early you probably would have made the cut-off, but if even one of the machines had been working, it would have saved you at least twenty minutes waiting in line.
I imagine misconnects and "no-shows" galore were the order of the day that morning, so the gate agents probably were shuttling folks between the planes so they were probably filling each plane with stand-bys so they might not have wanted to check you in because your seat was probably already released to a stand-by at the gate.