Sounds like you have had the dreaded disel bug (which breeds in any water in the tank), I'm surprised it hasn't stopped your engine/s.
My mate had this problem and it caused some worrying situations when at sea. He has now applied a chemical after thoroughly cleaning and drying his tanks, which seems to have cured his problem.
Once I get hold of him I will post the details of the suppliers (I know they are in Bromsgrove and the stuff was about 50 quid for 2.5 litres.
