Hi,
Correct me if I am wrong but I think he does not mean the mission section on the forum. I think he means that, after completing some missions, he clicked on the "custom missions" option ingame. Maybe expecting some "special" missions or something, but only finding an empty list.
So kligan, to use the custom missions, you must first HAVE custom missions. This means you either have to create missions of your own, using the mission editor, or download some user made missions.
If you want to create them, then you must update your game to v1.1 and download the mission editor. If you want to download community made missions, then you must do what groennegaard said. After registration you can than acces the "Missions" section.
When you have downloaded custom missions, put them in your "../Shipsim2008/Missions/Custom" folder and they will show up ingame when you go to "custom missions". (I think the retail version had another path though, the one I stated is for v1.1, someone will correct me if I am wrong, no doubt)
Go here for the patch and editor: http://www.shipsim.com/downloads/patches.php?PHPSESSID=94beff0c67ab9e0ce9da89f51a28b0ee
Regards,
Fred