When I start the game up, my previously configured controllers are triggering incorrect behavior!
This is due to the order in which controllers are initialized – the order can't be preserved from session to session. Unfortunately, there is no automatic fix for this.
This should primarily be an issue if you use different kinds of controllers (for example, an Xbox controller and a PS3 controller) at the same time, because different kinds of controllers have different button ID's. If you use the same kinds of controllers, their button ID's are the same, so you should be fine. You might have to swap controllers with another player if you want a specific player color.
If you are using different kinds of controllers, there is a manual fix. Before starting up the game, disconnect the controllers, keeping in mind the order in which they were initially connected. After starting up the game, reconnect the controllers in the order in which they were initially connected. Then everything should be fine.
Any more questions? Post them as a comment and I'll answer them!