i can copy boots disks and boot disk games but not self booting games. anything to do with mode 1?

i can copy boots disks and boot disk games but not self booting games. i just do a straight copy for games requiring a boot disk and they work. i can also copy working boot cd's using "mode 1" on disk juggler but how do i get self booting games to work? do i use the same "mode 1" settings? at the momennt they just show up on my dc as big 74 min audio tracks, any advice?