Well, if Script B is web-based -- by which I assume you mean that it should be accessed via a web browser -- you can't just run it from the command line.

I think the simplest thing would be to write a script that opens the web site and then runs the GUI app. This should be trivial with a shell script.

#!/bin/sh
mozilla -remote "openURL(http://your.url.here/, new-tab)"
/path/to/guiscript
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Since "perl2exe" suggests that you're on Win32, you probably want a batchfile like:

C:\Program Files\Internet Explorer\IEXPLORE http://YOUR.URL.HERE
C:\Perl\Bin\Perl  C:\your\gui\script
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