They may look the same but they're not. The wiring and physical spacing between the pins may be different. If they were all the same there would only be one type and there are 4 different types, balance adapters def are not all the same.

In your manual on page 8, it shows how to see the individual cell voltages. Hook it up and start the charge and look at the individual cell voltages. The voltage should be changing in both cells if both cells are being balanced. If you can't see both cells, the wiring change you've made is wrong. If both cell voltages are not changing, they're not being balanced and the wiring change you made is wrong. If it isn't balancing or you're not seeing both individual cell's voltage, it's time to get the correct balance board.

The are differences in the way the lipos balance wiring is wired. Differences in how they measure pack voltage and how they measure individual cell voltages. What look the same about a balance board is the surface where none of the wiring is shown. Turn them over and pull the insulation off to expose the traces and you'll see a Align is diff than a PolyQuest type adapter.

The only safety checks the charger makes is on voltage - that you're not trying to charge a 2S as a 3S and issues like that. There is some small chance the lipo was wired wrong at the factory, seen it a few times, but I suspect you get the right balance board, it will balance charge like its supposed to.