Almost all LiPos with 2 or more cells have a normal balance connector. The most negative wire in the balance connector (usually black) is directly connected to the thick black negative wire. The most positive wire in the balance connector (usually red, but can be other colors) is directly connected to the thick red positive wire.
The most negative balance connector wire is always all the way on one side of the balance connector and the most positive is always all the way on the other side of the balance connector. They are never the wires in the middle of the connector.
If that isn't it, you simply have a bad or reversed connection somewhere. Maybe a small pin bent over inside the shell. Maybe the wrong brand and the pins aren't long enough. Maybe you need to push harder to make it fully seat.
(With it all connected via balance connector) Get a volt meter set to 12 volts or the next higher volts scale and test voltages starting at battery balance connector and working your way out till you can't detect voltage any more. Learning to use a volt meter is fairly important in this hobby.