Tell us if you're using mods and have your SHIII patched to 1.4b. Then the guys might have a better idea what's wrong.
My thoughts off hand are:
1. The wrong patch. As most all mods today require 1.4b to work properly. Or you have the wrong 1.4b for your copy of SHIII. Check here....
http://patches.ubi.com/silent_hunter_3/
2. Conflicting mods.
3. More than 1 Super mod installed. As in one on top of the other... GW and NYGM installed at the same time, or something to that effect.