As to your original problem ForthRight, how are you setting up your game? I don't really play CTF (with bots or otherwise), but I seem to remember that when I did try it, setting it up properly was kind of tricky. If I put in the bots I wanted in the setup screen (even with equal teams enforcement off), when I started the game the bots seem to be randomly put on either team. I couldn't seem to get light side on one team and dark side on another, for example.
What I had to do was in the setup menu, decide how many total players I wanted and set all those slots to HUMAN. Then I started the game, which of course ment that only I was there. Then I went to the in-game menu and selected ADD BOT. This menu allows you to select which bot you want and which team you wanted it on. This allowed me to set the teams up the way I wanted. However, I don't remember what happened when the next game started. Give it a try and see if it works, and remember that I did this a while ago, so I may be a little off.