If this is a config file you control, I would change this to use real XML and parse it with XML::Parser or XML::Simple or something like that. Or, even something like Config::ApacheFormat (my personal favorite).

If you don't control it, I would change how you're doing it.

use strict;

my $config = '/var/www/cgi-bin/prt.cfg';

open( FH, '<', $config )
    or die "Cannot open '$config': $!\n";

my @servers;
my ($in_server, @temp);
while ( <FH> ) {
    next if /^#|\s/;

    chomp;

    if (/<server.*?>/i) {
        die "Entering server when in server\n"
            if $in_server;
        $in_server = 1;
    }
    elsif (/<\/server.*?>/) {
        die "Entering server when in server\n"
            if !$in_server;
        $in_server = 0;

        push @servers, [ @temp ];
        @temp = ();
    }
    elsif ( $in_server ) {
        push @temp, $_;
    }
}

close FH;

use Data::Dumper;
print Dumper( \@servers );
[download]

This can be seen as a very simple state machine.