Old DOS boot disk for W95?

I'm working to debug a minor but nagging lost step problem with my
Ahha-run mill. This is NOT a mechanical problem, nor is it electrical
noise. I suspect the computer it's running on as the root of the
problem. To test this, I copied all the needed files to another P100
system I have that is setup with W95. I then made up a boot disk off the
DOS computer that now runs the mill and tried to boot the computer.
Well, it boots, but when I try to log the C: drive, I get an error
message regarding an invalid drive spec. Is this because W95 using
something other than FAT16 file format? The bios shows the drive during
inital boot up.
Ahha needs a clean DOS system, not a "boot to DOS" W95 variant.
Do I just need to install another HD and format to the older DOS format?

Thanks,

Jon