A job scheduler by nature is designed to run jobs in the background, as opposed to the foreground or interactively.
Thus, a program requiring mouse or keyboard input will not run correctly until it is modified. This is by design — any program requiring user intervention cannot be run in the background; how would you accommodate running a job everyday at 4 AM (besides enraging the tech that drew this onerous assignment)?
A good rule of thumb is any job that can be run under the AT command (without the interactive switch) can be run by the Argent Scheduler. This includes Perl scripts, VB apps, FTP transfers, etc.