I'll explain: You are on the Brenodi team with 9 other players the other team got 2. When you kill the enemy(in this case the Northern Faction) you will become one of them because of team balance. The annoying thing is if you are commander and you are deep behind enemy lines and some enemy runs at you trying to 9mine/bomb/deconstruct your CV then the first thing you will do is either: 1. Run out and shoot the basterd 2. Run over him If you run over him and even if you are inside the CV you will switchteams auto. Seriously can you please fix this? And make it unable to switch teams while being inside the CV or any other vehicle? I have seen many games of my enemy, my friends and my self lose because of this bug. As I mostly have not enough time to run back to the CV before it is destroyed :/
It also happens if the enemy stacks you, I am nto supposed to lose because all the noobs join the other team( in case my team) espacialy when I am comm or someone else is.
This is caused by a server plug in, it isn't present in standard empires. Don't play on servers with silly plugins like this and maybe the admins will get the message and stop using them.
I didn't think any of the servers had autoswitch plugins anymore. The problem is exactly as you described; the commander can be switched in certain cases. Maybe you were switched by an admin? Anyways, if it happens repeatedly, then its a poor server and the population will die.