They may well be carrying flight plans and other planning stuff from insecure computers to secure systems. It is almost de rigeur that security is increased until people can't perform their daily work without breaching the security system in some way. Everybody thinks they have done such a GREAT job securing everything, and then all hell breaks loose when they find out that general users have been moving stuff around on floppies, CDs, thumb drives, or whatever the latest technical wrinkle is, and voiding all the careful security procedures. Sometimes it makes such a big mess it winds up in the papers. I'll bet this was the same thing, the security honchos thought there was no need to mess with mandatory security upgrades, as there was "no way" any viri could find their way into the secure inner sanctum of their network. Ho ho ho!
Jon