I tested both NTSC-U Mega Man X: Command Mission [GXRE08] and the PAL (En,Fr,De)[GXRP08] versions, 1:1rips, and the game freezes during normal play.
However, I noticed that the american GXRE08 version freezes RIGHT after 5 minutes of normal play, 10 tops. On the other hand, the european GXRP08 lasted almost the entire first chapter before it froze on me.
The freeze seems to be completely random, sometimes it's during the intro FMV, sometimes when I'm walking around and sometimes mid-fight, although the last one is rare.
nintendont ver. 2.146 was used.
I don't know if my USB is the problem or not, although I admitedly doubt so because I've been playing normally other games. I should mention, I think, that Command Mission does not recognize the Wave Bird controller, only the regular wired controller.
Thanks for taking the time to read this.