I think we are all going to need to know what is installed between the DUAL ALLEN WRENCH LUG terminals on the PD9260C chassis and the main battery switch.

This is how I am wired up using my PD9260C, Remote DC Monitor Panel, BLUE SEA Battery switches, and Batteries. The TOP RED Wire coming from the PD9260C + terminal feeds my 12VDC Power Distribution Panel where all the 12VDC Fuses are located.

I have a 4AWG CABLE running from PD9260C DC OUTPUT terminals connected almost directly to my main battery switch which is around five feet away. About the only thing that would drop the 14.4VDC outputs down to 13.6VDC at the battery terminals is small battery cables being used or perhaps you have a DIODE BASED three lug BATTERY ISOLATOR installed in the mix. The high current diodes will drop the DC VOLTAGE by 0.7VDC which is almost what you are reporting... This device is NOT to be used with deep cycle battery installs.
You must use these SOLENOID types of BATTERY SEPARATORS to charge your deep cycle batteries.

What changes have you done to your BATTERY CHARGING system since originally installing the PD9260C and seeing the correct transfer of 14.4VDC from the converter/charger and the battery terminals. Where are you reading the 14.4VDC voltages. You should be reading this DC Voltage at the DC OUTPUT lugs of the PD9260C when it goes into BOOST MODE.
I am just poking around here for info...
NOTE: I am NOT at all familiar with the TM500A Battery status monitor panel or how it is wired into the system so I may way out in left field here with my observations. My DC monitor Panel is a homemade meter panel using two each 12VDC meters and a +/-75AMP DC Current meter. My Battery Monitor system would not support a CURRENT SHUNT DEVICE installed in the NEGATIVE BATTERY LEADS as the TM500A monitor system requires.
Roy Ken