Possibly the problem is you have double quotes ( which will interpolate on it's contents) around my $output = "C:/Users/Desktop";

Try

chdir  'C:/Users/Desktop' ;
print pwd, "\n";  # see if it worked
#or
my $output = 'C:/Users/Desktop';
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notice the single quotes.

If it still gives you trouble, specify everything as full paths in single quotes, until you get it to work without the chdir. You can always do a "print pwd\n" to see where you really are.

my @args = ('start',  
                       'C:/Users/Desktop/file.exe' , 
                       C:/Users/Desktop/something' );
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Once you get it to work with absolutes, work your way backwards and substitute the variables, and check pwd after any chdir attempt.