Could it be that you also have mp3 files in there. Iirc the game can't handle the 2 audio file types simultaneously. Or maybe it can, but not as well. Either add them all as Ogg or all as MP3.
Or maybe they ended up in the wrong part of the folderstructure. Did you add it with JSGME?
[EDIT] The last is probably the cause. It should go into: C:\Games\SilentHunter3\data\Sound\Gramophone
Not into the music folder!
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