A possible reason for the discrepancy between the batteries is that there could be voltage drop between the main batt and the auxillary batt. Try a thicker gauge cable for the connection between auxillary and main batts. Also, get rid of the 400w inverter and use a dc-dc m2/m3or m4 atx psu as these type of psu's are designed to keep a consistent 12v to the pc even when battery voltage drops below 11volts or more and are more tollerant than a normal pc psu.
Most desktop pc motherboards run on 12v dc anyway so having an inverter will only use more battery power to boost from 12vdc-240vac to your desktop psu which then converts the 240vac power back to 12vdc to the motherboard. So dc-dc psu is strongly recommended. It will make the system more stable and will use less power than inverter.