I also had hart time checking in last year, before 9-11. I think it was SFO and with AA. The agent thought that the date change had to be revalidated and started calling all the places she could imagine. Took about 30 minutes to check me in finally.
It was then I decided that I should insist on open-dated segments at least for AA. I never had a problem of this kind with BA/CX/QF.