What you need is a different way of starting the Perl program in Windows. You can make a .bat file with a START command:

START      ["title"] [/Dpath] [/I] [/MIN] [/MAX] 
[/SEPARATE | /SHARED] [/LOW | /NORMAL | /HIGH | 
/REALTIME] [/WAIT] [/B] [command / program] [parameters]
[download]

The /MIN flag will start the command in minimized mode. read more here: http://www.robvanderwoude.com/ntstart.php

There are other links..this was first one I came across. This command was introduced in NT4 and is available on 2K, XP, etc. Note that it can also specify the priority. If your script causes any performance problems, use the /LOW option to explicitly lower the process priority to lower than normal. There are many more priority levels available in Windows, but these few are usually enough! Default of normal usually is the ticket.

Update: there maybe some way to type this command into some box in the scheduler..but if not make a .bat file and start it.