I seem to recall this being in the Perk/Tk FAQ, and they have a snippet of code you can place at the top of your script to fix the problem.
But another option, and the one I prefer, is to make use of the wPerl executable provided by ActivePerl, which will not show a command prompt.
Then I just make all my GUI perl scripts end in 'gpl', and associated 'gpl' with wperl.
Now your scripts will work the same everywhere, and you can still run them with perl to see any console output (which will be discarded when you use wperl).

Hope that helps!

--Glenn