Have you used a hydrometer on the batteries to test each cell? Easy test to see if one cell is completely out of the ballpark. I've also used a meter to test individual cells by attaching a piece of copper wire to one meter lead and dipping the wire into each cell while the other meter lead is attached to a battery post. The reading should be 2.0 - 2.1 volts on the cell closest to the post the meter is attached to and another 2.0 - 2.1 for each of the next cells e.g., 2.1, 4.2, 6.3, 8.4, 10.5, 12.6. If you get to one (say 4.2 on the second cell) and the next one doesn't add up (say 4.6 0r 4.8V) then you've isolated the bad cell.
You really need to check the health of each cell of each battery. Sounds like an intermittent bad cell on one battery. It will show up with an individual cell test - quickly.
One bad/shorted cell on one battery will drag the other battery down - either to its level or close.
Get out there and test cells - then get back on here with your results.