Why is the output always going to stdout?

Because it must not be going to STDOUT ( backticks capture STDOUT ), it must be going to STDERR (backticks don't capture STDERR )

Observe (I'm also on windows )

$ perl -le " print 111, `perl -e print(666)` "
111666

$ perl -le " print 111, `perl -e warn(666)` "
666 at -e line 1.
111
[download]

You want to use glob "C:/*.sys"

glob "C:/*WINDOW*/*.ini"

or File::Find::Rule, Re^2: code for serching .txt file through directories and sub directories, Re: list of files in subdirectories

or use Test::Compile - Check whether Perl module files compile correctly

What is is that you're really trying to do?