Sounds like the battery sense wire isn't connected, or connected wrong.
Battery sense wire is the smaller of the three wires in the output cable. With the D plug, it is connected to the auxiliary contact (Item 36 in drawing) and touches outside of Negative Radsok when plugged into cart.
Either connect it to the Negative (Black wire) terminal in the SB-50, or inside the charger, connect the black wire coming from the control board to Ammeter.
Here are a couple of schematics showing a PW-II type charger with three wire and with two wire output cables connected.