Hi Roger
You have the same problem as myself and the companies involved are the same.
I am live aboard and had a terrible time last winter with the unit continually shutting down until it would not start no more.
I had my very nice local eberspacher engineer (who i now know on first name terms due to the amount of times he has visited, he plays in a Dire Straits tribute band :-D) replace the burner and told me I would be wise to run my unit on parafin or derv or try fuelset additive. I tried using fuelset and when my unit was serviced for its first year the engineer said that the unit was well coked up and would fail in time if I didnt switch to another fuel source.
I didnt want another cold winter so I bought a jerry can which now lives on the swim next to the deck drain. He fitted a stand pipe into the jerry can and I have taken the copper pipe from the main deisel tank which feeds the eberspacher and connected the pipe to a tap which is fitted to the end of the stand pipe. This is a very crude work around and not a permanant solution but I have not had one problem since.
I have had my unit for a year, problems so far with my unit which is still under warrenty include , a new control unit, a new burner, new glow plug, new flame sensor, new air blower. Some of these are not all fuel related and my engineer thinks I must have just got a bad unit, he also recommended that I shouldnt rely on eberspacher as a main source of heat and should fit a secondary heat source which im in the process of doing.
I have done some research and found this article on fuel which explains about red diesel/gas oil versus derv/road diesel. There is more information around the web on the fuel issue.
http://www.vtt.fi/virtual/amf/annex_xxv/europe.htm
I am of the same opinion as yourself that there should be a seprate tank as this is what Gary suggest and builds into his boats and as a liveaboard eberspachers are not reliable enough and used to the amount of abuse they encounter over a British winter.
So I am also going to approach the NBC because they advertise there boats as liveaboards and I am of opinion that eberspachers are not up to the job of a main heat source, also why are they connected to the main red deisel/gas oil tank when the eberspacher literature clearly staes that there units should be run on parafin or EN590 diesel.
I will keep you posted
John