...Did they work to begin with?
Try uninstalling, and reinstalling ff7 for a normal, clean version. See if the games work. Then apply 1.02, and see if the games work. Then apply the high-res patch (if you use it) and see if they work. Then any other mods you may have, and see if the games work. Then finally, do the MGP (make sure to use the latest version). The thing is, MPG doesnt touch any code not related to either the snowboard mini game or bike mini game, so, it shouldn't be causing that your problems (then again, it also had a conflict with the high res patch and cait sith's slots, so, ya never know).
Though i'll play around; i dont think i've tried the sub mini game, either, so, i cant say for certain that it's unaffected.
Indra: I wasn't aware that it fixed the snowboarding crash, heh. I'll have to add that in. Though, as Grisu said, he's now having problems with the snowbaoridng, so, maybe that fucntion isn't 100% implimented...?
And ah yes, alternate fix information. Good idea =)