Whenever I minimze MBII with the launcher minimizer or with a 3rd part minimizer (Jedi Academy Minimizer v1.2) i get the message 'Jedi Academy Multiplayer has stopped working' and then the game closes.
Does base Jedi Academy crash when you minimize it?
Try disabling an antivirus, if you have any.
You can switch to MBII Client:
MBII Launcher => Settings => uncheck "Steam integration" (skip if there's no such checkbox) => Engine => MBII Client => Play.