Neutral ships are counted to your total tonnage, BUT they should not be giving you renown for them. Instead, you should be losing renown by sinking neutrals.
But dont worry, I'm quite sure I know what the problem is.
This one:
U-Boat:Battle in the Mediterranean Add-On
Just try and sinking a neutral without the add-on, you either lose renown or you arent given any, cant remember which way it was in the stock SHIII.