but the charging algorithm, the part that makes the regulator work smartly, is in the Link 2000R meter not the regulator box. The 2000R has to communicate well with the dist board and the reg module via all the tiny cable connections.

How is the start battery being charged? Via a combiner, diode isolator, battery to battery charger like an Echo or Duo or are you "directing" the charging via the battery switch? Does the alternator go direct to the house bank or through the switch? Where is the battery voltage being sensed for the regulator? Sometimes with these un-plugging and re-plugging the ribbon cable and phone type cables can make "issues" go away. It could also be the battery..