EDIT: It somehow escaped me that others had suggested effectively this very thing, although I did use a little used operator for printing out the DUP records, so technically it's a different solution! I so need to go home.

---

Is there some reason why just reading all the keys into a hash while incrementing the value wouldn't net you what you want?

my %hash;
while ( <IN> ) {
    $hash{ $_ }++;
}

foreach my $key ( sort keys %hash ) {
    if ( $hash{ $key } > 1 ) {
        print DUP "$key\n" x $hash{ $key };
    } else {
        print UNQ "$key\n";
    }
}
[download]