No conning tower? Sounds like Websters new "Fleetboat Stelth mod".
Low viability. However don't dive as it has a tendency to leak.
Uninstall the mods and see if everything is ok, if so add the mods one at a time to find which may be causing the problem.. Those mods are very stable so it may be something with your install.
The first thing that comes to mind is did you put the game in the Programs folder? If so I would uninstall that and put the game in it's own folder.
Set to run as administrator, that may fix your problem. Windows will run the game in Programs folder but when you try to mod it things don't work right.
Magic