I have the Uplay version of the game, but regardless this may help. From what I understand, the game is patched through a game updater that have to be manually run from one of the game folders.
Go to the actual file that the game is installed:
(This is how it looks on my computer)
Ubisoft -> SilentHunter5 -> Support -> GameUpdater
If you see a file called "gu.exe" then run that, though you'll probably have to be online for it to work properly.
Hopefully this works for you.