Charging While Towing

Trailer/running lights are not drawing from the trailer battery and are normally powered from the tow vehicle. If you were seeing 13.5-13.7 (normal range) on the vehicle but < 12.6 on the trailer you either have a bad connection somewhere in the battery charge line or upstream from the 7 pin. Did you meter the charge line at the 7 pin? It should mirror the voltage at the battery of the vehicle. That same voltage should be present at the battery bank on the trailer. If the voltage is the same at all points you had batteries that were more severely discharged then you suspected. That is a pretty big reserve you are trying to replenish basically on a float voltage level. You would need hours of bulk charging at plus 14.6-14.8 voltage to bring batteries reading 12.2 back to 90-100%. Your truck is not going to typically do that.