Make sure you don’t have the 3S balance leads reversed. It’s hard to see how the batteries are wired up.
This is how I do it:
I use single wire connectors – XT150 and AS150. Bullet connectors would also work. This makes wiring in series much easier. I have 12S (four 3S batteries). For charging, I disconnect the AS150 connectors from the ESC and disconnect one XT150 connector to split the 12S battery pack to two 6S packs, which I then charge with two chargers. The picture is showing one half of it.
In your case, this would be even slightly simpler since you only have 6S.