EXE Switches

I have a customer using our software on a windows 2000 machine. We have a Database program (for use with recruitment agencies) which links to a EXE file to send data over via FTP. One client out of hundreds has had an issue today with this program not opening correctly.

Basically the EXE file when run opens up to a config screen, when run with a switch should open up the App. However the switch is being ignored either by windows or something else. I have had the firewall (McAfee) disabled and configured but still it remaisn. When I create a shortcut to the EXE and run with a switch (bypassing our main app) the switch is still ignored.
Do we have any ideas what could be causing this to be ignoring switches or any tools that could be used to test this.