Mods not working... Help!

[sergei]

Originally Posted by Vaux

Now it says Silent Hunter 4 UBoat Missions and the graphic has changed to a surfaced sub with the sun in the background.

This indicates 2 things.

1. You are patched up to 1.5.
2. Trigger Maru has not been enabled properly

TMO has its own intro screen. You can't miss it.
It's very different from the SH4 U Boat missions splash screen, and says Trigger Maru on it.

Check that TMO is not double foldered inside your mods folder.
EDIT: Razark beat me to it. Check the link he supplied.