I'm sorry you lost a day of your holiday, but having done manual check-in several times for short and longhaul I can tell you it's a nightmare. It doesn't matter how much you practice (and in reality, it is just not practice to train in a live situation) it will take a lot longer than using the computer system.
The computer systems offer live updates on seat maps, pax figures, bag figures, special need entries, messages, printing of bag tags and boarding cards. Now imagine having to write all that down for say 250pax, how long do you think it will take? Exactly.
I expect the standby crew were called for the first out of hours crew whose a/c was ready to go.
Tough break for you though, but it happens sometimes.
Edited to add this link, not for today, but I expect it might be the same problem.
http://news.bbc.co.uk/1/hi/england/s...es/4430856.stm