239 people presumed dead by plane crash from Malaysia

But isn't the checking in process on a diff system? though that too is probably outdated

I assume this is in regards to the stolen passports.

I can't say what Malaysian airports have in terms of security procedures nor of their check in process, but I assume it would be a different and highly outdated system if people with stolen passports managed to get by. That kind of thing would never get past the terminal entrances at JFK International.