All the LiPo's we use are just a series of cells. The S describes how many of them there are. A 9S LiPo is just 9 cells in series so a 4S+5S and a 9S are exactly the same. This is just an awkward arrangement of balance connectors.
Often these kinds of batteries split the balance port in order to allow use with more common chargers which typically stop at 6S however if there's only 1 plug then you'd only be able to charge through the balance port alone.
It's important to be super careful when handling packs like this. What you described was shorting the battery to itself through the balance connectors. Inside the charger all the plugs are normally commoned internally with the other plugs. So plugging both connectors in is will short the cells from the first half of the pack to the second. You CANNOT plug both balance leads into 99% of chargers like that.
The charger is unhappy as I imagine from the 33V reading you have the main connector plugged in? In essence you are plugging in a 9S battery (beyond it's capability) but only giving it access to 4 or 5 cells for balancing at a time, any charger will be unhappy about this. You may be able to do a balance charge with the main connector unplugged if your charger supports it but it's going to be slow.
Chargers do go up to high cell counts but get pretty pricey. I'd personally recommend changing the battery packs rather than the charger as you'll then have a much more conventional (Therefore easier to work around) setup for future.
Not so important but: Another recommendation would be to bump the cell count up or down one to 8 or 10S so you can split it into a pair of 4S or 5S batteries and have both the same. Nothing wrong with having a mixed set but it's easier at events to deal with batteries when they are all the same.





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