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If it is possible to swap over the inputs that would confirm wether the unit B is the problem, or the array has an issue, a verification of sorts before sending it out on a warranty claim.1
The percentage has nothing to do with the self discharge, it is a recommended figure to provide sufficient PV capacity to support the battery. For every 100Ah of battery capacity, 10A or more, of charge current would be required . So in the planning stage of a system for a 310Ah 12V nominal battery bank, the PV array should have the ability to provide 31A thereabouts, so rough calculation 12V×31A=372W, panels generally produce 75% of rated output, so 372W×1.25=465W, this is the wattage of panels required, round it off to 500W.
In addition geographic location has to be taken into account, many overestimate the hours of useful sunlight, use this link to find the hours at your location, http://solarelectricityhandbook.com/solar-irradiance.html pay particular attention to winter months as this will be a determining factor. Please note all the above is a rough calculation there are many more contributing factors not included, the purpose is to point out that perhaps you have over estimated the amount the 2 ×100W panels are capable of supporting. Sometimes it's better to start from the beginning again with the loads, battery capacity needed to support them, charging system to support the battery, geographic location etcetera, etcetera. Most have made the mistakes, me included, with the help offered from various members, a successful system can be developed.
Here is a link to the Outback string calculator, all you need to do is enter your information following the instructions, attached pdf. this will give the optimal string configuration for the charge controller.
Your approach is unconventional, usually it is best to start with loads but as the items are aquired already you'll have to plan loads around capacity. For starters you will need MPPT charge controllers to work with the panels you have, so that would be a good starting point, once a decision is made then the current capacity, maximum voltage allowable etcetera, will determine the panel string arrangements. Quality charge controllers are the best choice Midnight, Outback, Morningstar, Victron, Schneider are examples, best to get one with local support, most are in the 60-80 amp, 150-200 volt input range, some 600V are useful if the distance from the array to CC is long. At least 2 or 3 will be required, best to research what's available and work with a specific models capabilities, once a choice is made.1
Being in the off grid category I assumed there was no grid, but based on the price of electricity in Tasmania, I can understand why you want to add solar, however using batteries solely will still cost more than grid. A grid tied system would be the most cost effective, even with the rates you pay, batteries have to be replaced every x amount of years, so the replacement cost is what drives the cost per Kwh higher overall.1