Here's what I worked out. It does actually work even though it looks like crap and I'm sure one of you can probably cut out half of the code. Please feel free to show me a better way to do this.

open OUT, ">$Output_Directory/sitescope.dat" or die "Can't open OUTPUT
+ file: $!";
foreach (@data) {
        $counter++;
        @tmp = split(/\t/);
        ($time,$date) = split(/ /,$tmp[0]);
        $date =~ s/2003/03/g;
        $time = substr($time,0,5);
        $mday = substr($date,3,2);
        ($hour,$min) = split(/:/,$time);
        $mod = int($min/5);
        if ($mod != $last_mod) {
                print OUT "$last_date\.$last_time\t";
                foreach (1..5) {
                        $seconds = $seconds{$_}/$counter;
                        printf OUT "%1.2f\t",$seconds;
                        $seconds{$_}=0;
                }
                print OUT "\n";
                $counter=0;
        }
        foreach (@tmp[1..5]) {
                $place++;
                $seconds{$place} += ($_/1000);
        }
        $place=0;
        $last_mod = $mod; $last_date = $date; $last_time = $time;
}
close OUT;
[download]

Original data:

08/08/03.07:55  1.61    1.158   0.71    0.209   0.535   
08/08/03.07:57  1.094   0.887   0.96    0.126   0.322   
08/08/03.07:59  5.131   0.986   1.029   0.095   0.251   
08/08/03.08:01  1.071   1.274   0.638   0.197   0.347   
08/08/03.08:03  1.166   0.984   0.598   0.092   0.583   

Chunked data:

08/08/03.07:59  2.39    0.94    0.80    0.11    0.30    
08/08/03.08:03  2.31    1.60    1.02    0.20    0.61