I'm assuming that you are configuring the logon script in the user's Active Directory object rather than in a group policy. Otherwise the users would not see the console session at all.
I don't know of a standard logon script configuration where the actual path to the batch file rather than the path to the command interpreter is displayed. See if the administrators in the other system have been changing the configuration with DOSKEY or some other utility.
This was first published in June 2001