One possible solution is to remove newlines when you're reading in the config:

if (defined($Config{$name})) {
  $Config{$name} = chomp $value;
}
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But that's really only a band-aid fix. As someone's already said, you'll have a lot less problems if you use CGI. Once you've got the hang of that, you might also want to look at HTML::Template, or one of the many other templating modules.