Are you using the cfg file in the Data / Submarine / SubName folder? Sprelling ez vury vury impore tent... So for something like the Balao, which does not have an interior of its own, it's interior line would be:
[Unit]
ClassName=SSBalao
3DModelFileName=data/Submarine/NSS_Balao/NSS_Balao
HumanPlayable=YES
Interior=data/Interior/NSS_Gato/NSS_Gato
...
since it uses the Gato's interior. Are you set-up that way?
Also, in Windows, caps, such as "Data" or "data" does not matter if the actual folder name is "Data". Windows can find it. With Linux or similar, character case makes a huge difference, so a "Data" folder cannot be found with a path with "data"...
