I may not be up to "Perlmonk" status yet. So I am assuming I am missing the problem, but if I wanted to test to make sure something didn't start with something I would use a little boolean if logic, like so :

if ($string !~ /^#/) {
  print "Houston, we have an uncommented line \n";
}
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Please do tear me apart if I completely missed the issue, only way a young buck is going to learn.