An easy way for this kind of problems is to reset the IRS $/, say:

use strict;
use warnings;
use Data::Dumper;

my %hash = ();
{
local $/ = "interface ";
while(<DATA>) {
    my ($key) = /description\s+(.*)/;
    next if $key =~ /^\s*$/;
    my ($value) = /switchport trunk allowed vlan\s*(.*)/;
    $hash{$key} = $value;
}

print Dumper \%hash;

__DATA__
.....
[download]

Make sure the IRS won't show up within each block, so make it more specific accordingly...
Regards,
Xicheng