I think it's simpler than that. He probably got
SH4: Wolves of the Pacific on Steam, but it's not updated with
SH4: U-boat missions.
Thus, Dark Waters (and most of SH4 megamods) won't work because the game is not updated to v1.5.
@Seewolf_ can you check what version is shown on the lower right corner of the Main Menu screen? It should be 1.5 to run Dark Waters.