Trimmed to the parts that use and modify @data:

my @data;
while ($running) {
    unless ($nfound) {
        ...
    } else {
        @data = split /\n/, $rawdata;
    }

    for (my $i=0; $i<=$#data; ++$i) {
        printf "data[$i]=%s\n", $data[$i];
    }

    foreach (@data,) {
        print "line=".$_."\n";
        if (...) {
            ...
            push @data, [ $name, $rrate, $wrate, $total ];
        }
    }

    my @sorted_data = sort { $a->[3] <=> $b->[3] } @data;

    ...

    @data = undef;
}
[download]

The outputs of the loops differ because you modify @data in the middle of it all.

Don't change the array over which you are iterating, and don't use the same variable for two different purposes.

Fix:

while ($running) {
    my @data;
    unless ($nfound) {
        ...
    } else {
        @data = split /\n/, $rawdata;
    }

    for (my $i=0; $i<=$#data; ++$i) {
        printf "data[$i]=%s\n", $data[$i];
    }

    my @parsed_data;
    foreach (@data,) {
        print "line=".$_."\n";
        if (...) {
            ...
            push @parsed_data, [ $name, $rrate, $wrate, $total ];
        }
    }

    my @sorted_data = sort { $a->[3] <=> $b->[3] } @parsed_data;

    ...
}
[download]

Note that I got rid of the @data = undef; by properly scoping my vars.

Update: Added more of original code.
Update: Added solution.