Tom, if frost is present on at least 90% of evaporator at any time now
then refrigerant volume is correct and to tamper with refrigerant now
can be an expensive mistake. Non destructive troubleshooting should
always be first. If a unit does run continuous and the evaporator
surface area covered with frost is consistently less than 70% then
there has been a loss of some refrigerant.

Because both systems seem to now be working then I would look at the
only common item between the two which is the boats wiring. Most boats
with dual systems like yours are not wired in dependently of each
other to the main battery buss, this means any trenchant voltage spike
from another circuit can signal a compressor module to cycle off that
compressor.