x2 on comparing water levels.
Re; batts 1 & 2,
Good job on cross checking individual batt V's! I had the same thing with one of my pairs of 6's. It does look like batt #1 is hogging some of the charge. This is yet another reason to split the bank... to see if this still occurs with the two batts in series only. Isolate batts 1&2 from 3&4. Connect the pos to batt #2, and the neg to #1, and watch to see if #1 still hogs a little more, during and after charge. This will help determine whether or not what Niner said is the case.
(I think this is where really good wiring and ends may come in to play? Less R between batts = more likelihood of a more even charge throughout?)
After I did a good EQ on the one 'unequal' pair, this stopped happening. The SG's tightened right up, and the V's came into line with one another. Today I'm wiring things back to series/parallel, so I will watch to see how the two pairs play with each other, during dis-charge, and to see if the batt with the pos wire hogs some of the charge, during re-charge.
As we go along, we learn what to look for. My log keeping has quickly evolved from simple time keeping, to Voltage comparisons, Amps to V drop comparisons, SG comparisons, etc. After a short while it becomes rather natural and easier than it sounds.
I'm still a little confused regarding your shunt set-up? Can you provide a link to the shunt you bought? Thanks!