what happens when you put a

print CSIDL_LOCAL_APPDATA . "\n";
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into your both versions? Does that show the same value? Also, are you sure the perl in your path is the same perl that is associated with the .pl extension?
That may sound dumb but i encountered that once. A guy in the office called me to assist in a perl error message.

Can't locate Something.pm in @INC ...
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Me: Easy. You don't have Something.pm installed.
He: (sighs) I know but I have written Something.pm It is there. Look. (and showed me the file c:\perl\site\lib\Something.pm
Me: Mmh.

I spend 2 hours searching for the reason. It turned out that this colleague had installed a "raw" perl (without installer or other such luxury). And because c:\perl was already used by AS Perl, he, in his wisdom, decided to install the second perl in c:\per1 and altered the path accordingly. So, when you typed

perl somescript.pl
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the second perl executed the script. And when you typed

somescript.pl
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or doubleclicked the script cia Explorer the AS Perl was in charge.