re
An automotive
regulator OTOH will simply reduce output as the battery voltage rises
toward the regulator set point, eventually getting to zero output
when the set point is reached.  This is perfectly adequate for
replenishing a starting battery which only loses a few per cent of
charge in starting; but for a house battery that is deep-cycle it's
an extremely inefficient way to do it."

My less techical way of looking at this is ...
your Zetec alternator with voltage regulator is designed to charge a regular
car starting battery.
Now, it is 'seeing' a much larger battery ...
and it probably 'appears' to the alt and regulator that it's battery is not
getting filled very well, since it's a,  whatever, 3 times larger battery
than it is used to seeing.

so the basic 'problem' seems to be the wrong type of voltage regulator for a
large house battery charging application.
or ..what David said. lol.