Hmm, now that I configured 1 ADF disk, no matter what other ADF's I click on, that original one is the only one that loads now. :/
Using real hardware? That's kind of typical... formatting a good disk in a bad drive allows for that disk to work, but only in that drive. Other disks formatted properly on a known working drive will not work in a bad drive. Overly simplistic, but there it is.
IF you're still talking about emulating... I dunno as I've never really buggered with it. My guess though is that maybe you're formatting a disk improperly (SFS with OS1.3, International, ??). Guess we need more info.