[XenonSurf]

If you are on the bridge and click on 'periscope depth or 'dive' or other submerged commands it will do nothing, you need to be inside your sub.

Do not ALT-TAB out of the game because keyboard commands will cease to work or grafical oddities can happen (invisible crew, messed-up teleport etc.) If it happens, save & reload.

For the TWoS mod to work correctly your game folder must be a non-protected one and you need all executables start in 'Admin rights' mode. For not setting all that manually it's best to install game elsewhere than the default proposed Ubisoft folder, e.g. C:\games\SilentHunter5.
Also not sure, but you may run into keyboard or font display problems if your system is different than US or European language settings; in this case set US keyboard (or German, or European) in Windows or change the 'Regional settings' in Windows>System to match your SH5 install language.