There are all sorts of actual reasons for online checkin not to work, and all sorts of crackpot theories, as well. I've found, for instance, that I can never check in for NW8602/KL602 LAX-AMS until the morning of the flight. A friend from AMS came up with the (semi)crackpot theory that, because equipment changes are fairly common on the route, and KLM runs several flavors of 747 with differing seat maps, they don't open online checkin until they're sure which plane they'll be flying.

Still, whenever I have trouble checking in online, I live in fear of SSSS. A fun SSSS story: Last month I flew AMS-SEA-LAX, with the last leg on Alaska Airlines.For some reason, NW couldn't get me a reserved seat in advance on the Alaska leg, and I didn't think to call Alaska directly. When the nice woman at the lounge in SEA finally got me a seat, the boarding pass came up SSSS. She called the gate and said the SSSS was her fault--she had to force the computer to give me a seat, which was interpreted as a last-minute, one-way booking--and they should let me go without the interrogation. It worked, bless her!