Maybe a simple approach?

use strict;
use warnings;

my @log = ();
while (<DATA>){
    chomp;
    push @log, $_;
    if (scalar@log ==3){
        do_stuff(\@log);
        @log = ();
    }
}

sub do_stuff{
    my $ref = shift;
    print join ":", @$ref, "\n";
}
__DATA__
1
2
3
4
5
6
[download]

Gives :

1:2:3:
4:5:6:
[download]

Argh. Only just seen your update... what solution did you go for in the end?