Hi Graham, to be honest I am a little confused as two machines are involved and much has been posted above. Therefore, I will simply list my thoughts, as this is how I would approach the problem
Ensure all master discs are write protected
On the machine that loads, are you able to copy the boot disk(s) and then will they boot on the same machine. This will prove the copies are good
On the machine that does not boot, can the drives be swopped (e.g.so B: becomes A
for test purposes. Maybe by just a Ribbon Cable move.
Floppy drives can be cleaned, my removing the top, then blowing out any muck with a Hair Drier set to cold and max blast. Use a long thin brush to assist. Gently clean the heads with a (bent) Cotton Bud dipped in IPA.
I think the os on least on of the machines is DR-DOS not MS-DOS.
Belief a CFI file is compressed, so files need be extracted before use.
When creating a System Disk with MS-DOS, the /S parameter need by used in order to copy the 2 or 3 hidden system files.
See note 3 here:-
http://git.net/ml/os.drdos.general/2.../msg00000.html
Good Luck - Mike