It depends on the amount of information on the MS-DOS diskette, but there
are probably some other factors involved to bring the access time to a full
minute. More than likely there are other INITs, CDEVs or applications (if
you're running under MultiFinder) that are stealing CPU time away from
Apple File Exchange. You can easily check this by starting up with a
floppy under Finder-only and launching AFE.
Another possibility is that AFE is running out of memory. If you're running
MultiFinder, try boosting the RAM allocation by 200K or so.