Invalid command.com

I have a problem with a computer running msdos 6.20 When
I boot through my config.sys and autoexec.bat it gives me an
error stating invalid command.com system halted.
If I boot clean f5 it seems okay. I cant figure out whats giving me
this ierror
JordanAsked:
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billogleCommented:
Your command.com is not the correct one for the msdos.sys and io.sys (hidden files).  Boot clean or use the F5 key to bypass the autoexec.bat &  config.sys.  At the C:\> prompt type c:\dos\command.com and press enter.  If prompted to overwrite answer: y

Reboot the system and it should work.  If it doesn't email me at bill_ogle@reborn.com and I will go into detail on the one reason why this didn't work and how to fix it.  
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