The Dark Waters display might say v5, but it is v6. There are a few "patches" that folks have made, but nothing major. Perhaps those folks will stop by later and point you at what they have done.
In the meantime, one of the seemingly strange things about the game, is that it runs off of the information in the Save folder, which defaults to "C:\Users \UserName \Documents \SH". If you play the game, and then add or subtract a mod, dependent upon what is edited by the mod you sometimes have to empty the contents of that Save folder to kick the game into updating the data it uses to run. You can either delete that whole SH4 folder in Documents, or just the cfg folder below that SH4 folder. Do NOT delete the game folder, just the folder.in Documents.
Also, Windows has a nasty habit since the Vista version, of protecting the Program Files folders from 'user intervention', which includes not only you, but Silent Hunter games and JSGME. If you are in C:\Program Files (x86) \Ubisoft \Silent Hunter..." or similar, such as "C:\Program Files (x86) \Steam \SteamApps \common \Silent Hunter...", then you will have to change your installation location to a folder you create yourself outside of the Program Files folders, such as "C:\Games" or whatever you want. See
Moving a Steam Installation and Games for their methodology. Depending upon your Windows and upon Steam, you might be able to copy the whole SH4 game folder, and then paste that into the folder you created yourself. You would then have to start it from the SH4.exe file in that folder, and/or create yourself a short-cut to it.
