You must not have any mods installed when installing U-Boats. And once you have U-Boats installed, it will break compatibility with just about every mod out there, especially super-mods like Trigger Maru.
The only mod I'm aware of right now that does work with U-Boats expansion is the new HUD colors mod by Jimimadrid
http://www.subsim.com/radioroom/showthread.php?t=131878