Found it...

sub ReadConfig()
...
while(@lines)
...
  # Store what our line ending char was for output
  ($self->{line_ends}) = $lines[0] =~ /([\015\012\025\n]+)/;
  while ( @lines ) {
    $_ = shift @lines;

    s/(\015\012?|\012|\025|\n)$//;                # remove line ending
+ char(s)
    $lineno++;
    if (/^\s*$/) {                # ignore blank lines
      next;
    }
    # added this... ignore registry values
    elsif (/^HKLM/) {                
      next;
    }
    ...
[download]

It works now. Thank you :)