GEM e825 quiq charger connection issues

I have an early 2000 model e825 purchased new way back then The charger died so the local Polaris dealer installed a new Delta-q 912-7200-02. I’ve struggled with getting it to perform correctly with different fault codes. I disconnected the front 2 batteries and utilizing jump wires I made reconnected them in series with the 4 batteries under the back seat. connected the charger directly to these batteries and the charger seems to be working perfectly. start up process is normal then goes to full level charging rate on the ammeter.

With the batteries installed for use in the car and the charge wires connected to the control box closest to the steering column the charger doesnt work correctly. btw using trojan batteries and profile #13. when i plug in to start the charge the start up process on the charger is normal then the bulk charge light is on, and first level ammeter light is on. after a few minutes the charge complete light blinks green and the first level ammeter light blinks too and the batteries don’t fully charge.\

I think my problem is wire connection. not sure where to start?