I got the clunking niose too, but I assumed it was to show the ag of the boat, because all I ever got it on was the S-Boats.

For what it's worth, this problem only happened for me when I had the Ultimate sound mod installed. I replaced that mod with the Flavored to taste mod (which contains a lot of the same sounds) and the audio looping went away.

I thought the reason for this was that you can't have sound files longer than 15 secs?
That clunking sound probably comes from amb_SubmarineInterior.wav in \Data\Sound, open it and check the length.

But Some players have the same problem without mods :-?

I checked all my looping sound effect files and I believe they are all less than 15 sec. I still get the clunking. It happens about 50% of the time I exit time compression.