weird... I always put custom textures in the textures\tnormal\tex folder. And I've never had any problem with textures not showing up.
Were you working in your normal game folder (...\Silent Hunter 4 Wolves of the Pacific\Data\....) or a different directory? Cause probably S3D can't find the textures folder if the texture folders are placed in another directory (e.g. ...\AnotherDirectory\Data\textures\...).