Some mods will have other folders than what the game has, such as 'Extras' or similar. You might also see a ReadMe dot text file. However, you should not see other extra files. As ETR3(SS) says, check your mod folder structure. Also, be sure you have the proper version of Silent Hunter for the mod. Some mods are for v1.4 or v1.5 only, others are for both...
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JSGME (Jonesoft Generic Mod Enabler)