Hi illutic,
I have exactly the same problem: after upgrading to 2.8.4 my main and sub categories got mixed and appeared in alphabetical order. Apart from that the My Category Order isn’t working at all, but that’s another plugin so another topic I guess (I get a completely white screen when I activate the My Category Order, even after re-installing it).
I would love to hear which function you added to functions.php and what you mean exactly by calling it per main category… (I’m not a programmer so if you can write it down more detailed I would be pleased :)) Still wondering why every WP upgrade always comes with plugin problems…