Start computer with the bootdisk. At the command prompt type in
path c:\dos
and press enter. This will tell the computer where to look for the commands you are about to type in. Now type in
dir c:\command.com/s
and then press enter. This will show you all the occurrences of command.com on your harddisk. There's probably two, one is in the root directory and the other is in the dos directory.
If there is two, rename the one in the root directory to command.bad like this
ren c:\command.com c:\command.bad
and then press enter. Then copy the one from your dos directory to the root directory like this
copy c:\dos\command.com c:\
and then press enter. Before doing any of this you should run scandisk using the autofix and surface switches first like this
scandisk c: /autofix /surface
and then press enter.
HTH