To chime in here for what it's worth, Mooch says that in a para-series configuration, each pair of cells in parallel will balance each other's voltage, just like in a regular dual parallel mod, but the 2 pairs being in series with one another will not.
In other words, what your charger is telling you. Slots 1 and 3 were a parallel pair and slots 2 and 4 were the other pair with the pairs running in series with one another.
In OTHER other words, it would only take one cell of the pair in slots 2 and 4 to be weak for it to pull the other one down some as they balance each other.
OR, the mod just discharges unevenly
I don't pretend to have more knowledge than you do, but maybe it's been a while since this has been on your radar.