My situation is just a little different. I'm running a batch file on startup to distribute the latest version of internal business applications.
In this situation I'm using the Windows Registry Run Key with the following string
cmd /c copy \\serverName\SharedFolder\startup7.bat %USERPROFILE% & %USERPROFILE%\startup7.bat
This runs two commands on startup in the correct sequence. First copying the batch file locally to a directory the user has permission to. Then executing the same batch file. I can create a local directory c:\InternalApps and copy all of the files from the network.
This is probably too late to solve the original poster's question but it may help someone else.