>May be the path to the batch file contains spaces something like:
>c:\program files\BatchFile.bat
>If it so, you must not use a macro (&) but parenthesis ()
>
>RUN/N (MD5BatchFile)

No, I know that the batch file runs, as I can add a command like DIR /p at the end and the dos window will freeze. I can then see the results of the cd and md5sum commands, and they are something like 'directory does not exist' and 'file creation failure'. It just seems so odd that the exact same bat file works when run from windows explorer.