I figured out so I'll reply incase others had this prob, I changed 3 things at one, I'll list them in order of likelyhood that that was the fix:
1. I deleted the M3's .dat save file, meaning the m3 says it failed to save minivmac.nds, but ofcourse because the program edits the .dsk file, it doesnt matter, I think this is what fixed it.
2. I downloaded a pack from a homebrew site that had different .zip names and everything the Lazyones site, i'm not sure if it has been modded for the M3.
3. I didn't rename the .nds like I usually do.
Seems to work perfect now, I think it was the .dat that ****ed it up.
Bookmarks