Actually, the issues you describe are UT2004 issues, not Chaos, and certainly not SubMagma (I don't know that the bot pathing in SubMagma is "perfect" - but it is not the cause of the problems you are having).
vCTF in UT2004 does not have proper bot support, and currently there is nothing you can do about it, except make maps that have poor layouts for human play.
I am rather informed on this topic (I'm not even a mapper, but I have read such things as Blitz's tut, and the comments from Mr. Polge, and I'm aware of such things as the 'white road'), but if you don't want to take my word for it, play many VCTF levels and pay attention, this is what you will see. OR, you could read comments from experienced VCTF mappers. For example, this Atari thread has a comment from another mapper who made several VCTF levels, some of which I didn't really care for that much, but now I see that he was aware of the issues was well, as was just as unhappy with his maps layouts as I was.
http://www.ina-community.com/forums/sho ... genumber=5
He goes on a bit, but the bottom line can be summed up here:
Toonces wrote:If the A.I. can be corrected, I would love to see vCTF really take off as a game-type
You cannot make the bots work in a VCTF map in UT2004 unless you allow them to drive right up to the flag. Most of us CTF'ers realize that this is not good for game play - not at all.
Thus, the issues in SubMagma. Naturally, as lead tester, VCTF fanatic, and someone who pays attention, I was well aware of the bot issues with SubMagma before it was released. I did not however recommend that the map be withheld, because it has a good layout for human play - making it play good for bots would have ruined that.
(If you have a good machine, ask Hammer for a version with the original layout, which had these sort of suspended roadways going around the top of the map. It doesn't improve the bots any, but IMO it was a much better layout for humans. Unfortunately someone complained about FPS issues, and he took those out in an attempt to help. I was not pleased.

)
Another reason I supported the map was because I had assumed/hoped that either Epic or Chaos would have taken it upon themselves to fix this issue by now. Sadly, neither has happened, and UT2004 is missing the boat when it comes to this extremely popular game type.
And it's a big boat.