Unless the GA checks off your name - you are not going to show up on the flight. Usually if the GA's are not logging you in as you board, they will tear off the top part of the co.com printed sheet. They have got to record it some way, check you off, etc.

The only other option would be to compare the number of people who have checked in and count the number of people on the aircraft and if the two agree - then they say everyone is on board. I suspect the FA - in your case - likely saw your sequence # and keyed it in right after you walked on board. Many times the computer printer boarding passes do not read very well - they are not scaled the same as the kiosk printed pass.

A situation I observed at SAN a few weeks ago, was that as FC boarding was announced - a woman just walked on board - not through the elite access line and the GA did not see her - since she was collecting Elite access boarding passes.. She (a Spanish speaking woman - who spoke English) was seated one row behind me in F - so I mentioned as I was ready to sit down, that she should let the FA know that she is on board. Otherwise her seat may be given up. She let the FA know, but apparently he did not do anything about it - just told her - it was OK. With the flight running late - because of the usual delayed boarding at SAN (eventhough the inbound was there with plenty of time) - already 15 minutes pass departure time - an announcement was made if the following 5 passengers were on board and they came around and checked. Sure enough - this woman - was not logged as being on the flight - since she just walked on (great security at SAN). Again all this delayed the flight even more.