I suspect that your 16 100 AH batteries are wired in parallel rather than series, otherwise you'd have ~200 volts instead of 12.
It is possible that one (or more) of your batteries has developed a shorted cell - I had this problem on my boat. The voltage would not get over 12 volts, even using a high power charger for a long time. I eventually noticed that one battery required lots of water in all but one cell - once I disconnected that battery, the other battery quickly came up to ~14 volts under charge.
If you have normal flooded cell batteries, check the water levels,looking for batteries where one cell doesn't need water, but the rest do - that (or those) batteries will be bad, and removing them from the bank should allow the rest to charge normally.
If you have "maintenance-free" flooded batteries, you may be able to pry off the cell covers to do this check.
With gell-cell or AGM batteries, you'll probably have to disconnect batteries one at a time to find the bad one. With the batteries disconnected, measure the voltage of each one to find the bad one - its voltage should be about 2 volts less than a good battery.
It is generally recommended that all batteries in a bank like yours should be the same vintage, and have the same usage history, so you may want to replace all the batteries at once, rather than one at a time as they fail.
You should be using "deep cycle" batteries (often called "marine" or "RV") for this application. Many boaters use 6 volt "golf cart" batteries connected as two 6 volt batteries in series, with several pair in parallel as needed for the desired capacity, for deep-cycle applications.