Availability and reliability of passenger lists
 

One of the conclusions of the inquiry by the Dutch safety board into the crash of MH17 was that "reliable passenger lists are not easily available in international civil aviation".
I am wondering how this can be: every time I check in (online, via a machine or at the airport with a check-in agent) my full name and other personal data (usually date of birth, nationality and passport number) are registered. One would assume that at the time of boarding, and before the aircraft doors are closing, a passenger count is done and any missing passengers are taken off the flight manifest.
So why isn't one push on the "print" key of a computer sufficient to know who is/was on a certain flight??

Good question, particularly in light of the A380 flight that just got re-routed mid-flight because the crew didn't discover until they were in flight that they were two passengers short.