There are two different engines to run game with,
- JAMP
- MBII Client/OpenJK
Steam = JAMP.
When starting game via MBII Launcher, you can choose what engine to use:
MBII Launcher => Settings => uncheck "Steam integration" (skip if there's no such checkbox) => Engine.
JAMP stores its settings here:
Jedi Academy\GameData\MBII\jampconfig.cfg
And MBII Client stores them here:
Jedi Academy\GameData\MBII\openjk.cfg
My Documents\My Games\OpenJK\MBII\openjk.cfg
btw, in fact there is another one engine, jaMME.
It's great for creating gameplay videos.
Also MBII Client is fork of OpenJK, so theoretically, we can count pure OpenJK as fourth engine, though I doubt many ppl use it anyway.
Related thread:
OpenJK vs JAMP