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It may not seem like it should be but this is the expected behavior when you join an already in progress match.
When you first joined, the balancer noticed one team was down a player so it immediately put you there. At the next check, it noticed that your joining the match created a large strength difference in the teams so it then calculated that swapping you with a player from the other team would result in an evenly matched game based on the player strengths of each team.
It would be too disruptive to the game to swap you with the other player when you first enter for at least two reasons.
- People often join and then leave almost immediately so swapping players whenever this happens wouldn't be good at all.
- Some losers would notice this behavior and be forever reconnecting forcing players to be swapped all the time ruining all the games.
There is just no way around it. If players are allowed to join the game late or leave whenever they feel like it, some movement of the other players will need to happen to try and keep a moderately balanced game.
If you really aren't okay with the server putting you on the other team ever then it will be best for the other players if you just don't join the game at all.
You just have to except it, like everyone else does, and stay on the team the balancer assigns you to whenever it happens.