T&T: Fuel Tank Woes

[Key Stage]

      I have been a T&T subscriber for the last year, and cannot thank everyone enough for all the excellent information I have received from so many.  I now find myself in need of help in a somewhat urgent situation.  My Lord Nelson Victory Tug ( Cummins 4BT3.9M turbocharged diesel)  was purchased last fall, and the old black iron fiberglass fuel tanks needed replacement because of fuel leaks.  I learned from this list that once one goes, the others are soon to follow.  I read everything I could about fuel polishing, tank material, etc.  Over the winter, I had three new aluminum tanks fabricated, new ventilation lines each with Racor LT100 fuel/air vent line filters for protection, and a fuel polishing system made to Captn. Wils specs using my dual Racor system with a supplemental  high flow pump.  My fuel gauges are Hart Tank Tenders, so it has been difficult to know exactly how much fuel is in each tank, but I assumed this would be a trial and error process determined
 by engine hours and no. of  gallons put back in the tanks at time of refilling.  I have noticed that it seems very difficult to fill the tanks.by going slowly the port and starboard fuel fills seem full and bubble to the top.  So, I assumed the tanks were full.  Indeed, the Tank Tender indicated measurements of about 10-15 inches in each tank at the dock.  But, after leaving, the levels would drop to around 5-6 inches in the starboard tanks, and remain at about 15 inches in the single port tank.  Yesterday4th of Julymy wife and I decided to cruise down to Boothbay, a trip of about 40 nm, and I wanted to fill up my tanks before leaving.  They would only take 5 gallons, but the Tank Tender indicated 15 inches or so in each tank.  The fuel came from a very reputable marina where even the USCG fuels up, so I do not suspect contamination.  After a perfect 6 hr. trip without any problem, as I pulled into our reserved marina slip, the engine began sputtering and idling
 roughly.  I barely was able to dock, and used my bow thrusters to save the situation.  I suspected fuel problems, and indeed both Racors had sludge in them, and the sediment bowls were full of water.  I changed both filters (2 micron size), drained the bowls and turned on my fuel polishing system (valve diverts fuel flow from the engine and circulates back to tanks.  Immediately both bowls filled up with water again.  I suspect the port tank is the culprit, but I just do not know how to proceed from here.  Naturally, the holiday weekend means that the shop in my home town that did the work is closed.  I assume I need to hire someone to fuel polish my entire system, but any ideas what has happened?  Why is it so difficult to fill my tanks?  I assume that the tanks never did get full, and allowed condensation to accumulate, but can it be this much water from condensation alone?  Or, do I use my own fuel polishing system and just keep going through Racor filters and emptying
 sediment bowls until the water is gone?  Very frustrating considering the amount of money I spent just to avoid this very problem.  I write this at 3  AM because I cannot sleep trying how to rectify this situation.  Thank goodness it happened as we arrived rather than in a narrow rocky passage here in Maine!  All this on our very first overnight trip!  My thanks in advance for any suggestions either on or off list.

Key Stage
  m/v  TITAN.temporarily (I hope!) in Boothbay, ME