Hi Meeruelle
I've had Sh3 since the day it was released and can honestly say that I've
never had any major problem with the comparative volume levels of the game sounds.
It has always seemed to me that the original default levels:General,Music,FX all set to 0db,Speech at -10db, are pretty much ideal.This assumes, of course, that there is no hardware problem with your sound card. The only adjustment I make on the sound options screen is to uncheck the Music box.
This isn't to say that individual sounds can't be too loud, or too quiet for your tastes. You can have a quiet gramophone ogg file or an extremely loud effects wav file. Example: some mods have a diesel engine sound like a squadron of tanks going up a 1 in 3 gradient at full throttle. U-boat engines didn't sound like that - unless you happened to be in the engine room. And the creaks noise levels are generally completely over the top!! IIRC, in Das Boot you didn't hear any creaks until the boat got down to 200 meters or so.
In cases like this it is probably better to adjust the volume level of the individual file. For this you will need a sound editor programme. It's usually pretty easy to make a simple volume adjustment with one of those.
Ooops,I'm rambling too much.

What I should just have said - is that if you are adjusting the volume buttons to get rid of some particularly annoying effect, to increase the volume of something you like,or to make up for a hardware deficiency, then that may not be the best way to go about it. It's possible that you could be messing up the overall balance.