Thanks guys. Like I said, I did go ahead and convert all of my mame vids just with a ffmpeg script. I have heard of handbrake and have used it to convert mkv to mp4 before. As of now, the flv files work for all of my other systems, since only mame has vertical snaps. Doing my conversion, I noticed the mp4 files are a bit smaller, so I may go ahead and convert them all anyway to save some space.
Thanks again to h0tw1r3 for helping me figure this out and to akafox for the ubuntu debs all together.