Check your Sh3.exe in your games root folder.
(should be C:\games\Ubisoft\SilentHunterIII - don't install into default path)
Rightclick -> Properties -> Tab Details - if version reads 1.4.0.1 your game is patched to 1.4b.
If you have to patch your game - use only 1.4b and choose your correct patch file.
US - for DVD or Download
EMEA (Europe, Midle East, Asia) - for DVD or Download
http://silenthunteriii.com/uk/updates.php