Switch the docking cable of the powertube directly to the BDU, check if the system responds as normal, if ok, check the Y cable to both docking cables and cross them to see if one of the batteries does not start charging when the charger is connected to the charging port.
We have had bikes with 2 powerpacks and 1 powerpack and 1 rackpack for BES2. Those setups are a bit different I think because you lost one charger port I recall?