Works for me like this ...
 

C:\Ubisoft\Silent Hunter 5\MODS\"mod name with folder" and JSGME.ini file with all the Mods listed as text file , you can open it in notepad to see if the Mods' list is there or can add the same mod folder name as text list in the .INI file.
I also have the C:\Ubisoft\Silent Hunter 5 ..JSGME.exe and .ini files in the main folder

hope it helps :)
cheers!:)