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The other two possibilities that come to my mind,
1) Try to find out what NAV is trying to do; is it trying locate these files on the client or on the server?
2) Permission issue: Does the user account which is running the NAV service have access to these folders and files?
Other than this I am not able to think of any other problems.. however, I would again like to rephrase one of my questions,
where is this d:\upload.bat or d:\upload.cmd file? If it is on the client from where you are trying to run, then, are you sure that the NAV client is not trying to find this file on the of the server?