I think now the charger doesn't know how much of the R it sees is from the wire and how much is from the battery. We do know that as battery R climbs, at some point amps taper, and when they do, input power required by the charger drops.
So IMO (for now :) ) if the wiring R is so much that amps are lower, then the power input to the charger would be less.
Testing for that, be sure that the input 120 voltage remains near 120 so the lower amps you see is not in any portion from lower voltage input. Also the batteries must be at low enough SOC and big enough in AH to accept the charger's max amps if they can get there.