Some thoughts & questions..

#1 Solar has a very nasty habit of tricking battery monitors into premature resets. They reset on current, time at current, voltage and time at voltage. Late or early in the day it is very easy for solar to mimic a shore charger or alternator in float mode and the battery monitor resets prematurely... If you have solar I strongly advise programing your battery monitor to NOT auto-synch and switch over to manual synching which is far more accurate especially when you have solar or wind..

#2 The only truly accurate way to know your bank is "full" is to use the net battery current flowing into the battery at ABSORPTION VOLTAGE.. This is very, very simple. Absorption voltage is 14.2V - 14.4V or with some batteries & 14.6V - 14.8V with some others. 13.8V is not an absorption voltage and the current flowing at 13.8V will be considerably less than at 14.4V. Any voltage below 14.2V is really not a suitable absorption voltage unless you have GEL batteries. You can not accurately reset a monitor based on net-accepted current at anything below 14.2V but preferably 14.4V+... Well, actually you could but you would need to know the conversion from 14.4V net current when full to 13.8V net current when full. Problem is that if only ever getting to 13.8V you simply are not yet "full".....

In order to do a manual reset.

A) Fire up engine and run at high idle(nl)B) Be sure all DC loads are off(nl)C) Check battery terminal voltage, is it 14.4V at the battery terminals? (if not you may be chronically under charging)(nl)D) Look at the current screen on the battery monitor.(nl)E) If the net current flowing into the house bank is 2% or less of the 20 hour capacity the bank can be considered "cruiser full"(nl)F) If at less than 2% of "C" and also at 14.4V then you can now manually reset the monitor to 100% SOC.

#3 Many factory alternators today are coming through with self protective features that reduce output voltage as the alternator heats up. Reducing the output voltage also reduces the accepted current and is self protective of the alternator and helps it run cooler. Sadly this brings the term "dumb regulator" to new heights and with these alts on large banks they will chronically get under charged.. Your Valeo/Paris-Rhone may be doing this, some of them do. Some Valeo's even regulate to 13.8V and this is simply unacceptable and can lead to chronic undercharging.. You need a true absorption voltage. Most GC batteries actually prefer and do significantly better with 14.6V to 14.8V absorption voltages but for a dumb regulator 14.4V would be much better than 13.8V. With a smart regulator 14.6V to 14.8V is fine provided it drops back to float when or if the bank gets fully charged. A dumb reg won't do this so I prefer a max of 14.4V.. If you get 14.4V when full and the alt is cold and only 13.8V when the alt is hot this is your answer. A dumb regulator will stay at one voltage indefinitely. A temp compensated dumb regulator will drop the voltage when the alt heats up whether the battery is charged or not. This Drastically extends charging times and leads to chronic under charging. Whether you have a temp compensated dumb reg or a low voltage dumb reg this is an issue that should be addressed if you want good charging performance.

#4 The alt should ideally run to the house bank first, not the start bank. Every terminal in the path can be adding resistance and resulting in voltage drop in the charging circuit. Route all charge sources to the house bank first and this will give you the best charging performance of the bank that needs it most...

#5 I'm not a huge fan of "dead lead" or what you are carrying up in the bow to power your windlass. This lead would be far better served by adding it to the house bank as added capacity. You will get more efficient use of the system, shallower discharging of the house bank and benefit from the Peukert effect you get with a larger bank. In most cases, on boats under 40', it makes little sense to have a dedicated bank for a windlass or even a thruster. They use very little in terms of Ah's so carrying around a battery that will rarely if ever dip below 90% SOC is carrying around 90% of the bank as dead lead. You already carry around a bank of 99% dead lead in a starting battery. Yes the cables get expensive but you only have one bank to ever replace and because it is bigger it will last longer thus paying for the cables over time.

#6 Test the voltage drop your charging circuit when the bank is depleted or in bulk mode.. First place one lead from a DVM, set to mV, on the B+ terminal on the alternator then the other lead on the house bank + post. Fire up the motor and run at 1800-2000 RPM. Do you have a reading on the DVM? Ideally this should not be any more than 0.1V. Now repeat the same test on the neg cable by placing one lead on the alternator case and the other end on the batttery negative terminal. Do you have a reading on the DVM? If you have voltage drop on both pos and neg sides these get added together for your total voltage drop. Alternatively you can test voltage at the back of the alternator across B+ & B- then move the meter to the house bank and test voltage at the pos and neg battery terminals. If you have 14.4V at the alt you should have no less than 14.3V at the battery bank..

#7 How is your MPPT controller programmed? Absorption? Float? Internal or external temp sensor for the controller? Is auto-equalize turned OFF?

#8 Were your 6V batts ever commission charged / balanced? Have they ever been equalized or pushed to 15.5V?

#9 How hot does your battery compartment get? Are they in an engine space? Flag blue hull heating the batt compartment?

#10 Remember absorption and float voltages are always measured only at the battery terminals. Having the correct voltage at the back of the alt does nothing if the system is dropping voltage and you are not getting an absorption voltage at the battery terminals. Compare your 13.8V number to the actual back of the alternator.