PC re-boots when starting application.

I have 2 Windows 2000 computers, peer to peer. All service packs and anti virus files are up to date.
I have a drive mapped to the “master” computer and run a DOS application from the secondary. The application is started by a desktop shortcut that runs a batch file. The command line is
F:\amsi\w2\sysalt.bat
If I run this command line from a DOS prompt, it works fine. If I start the app by using the shortcut- Windows re-boots every time.
I have re-created the shortcut, installed a new copy of the batch file and re-mapped the drive. I have scanned for viruses etc. This is the only thing that causes a re-boot.
Any ideas would be appreciated. Thanks