use strict;
use warnings;
use GD::Graph::linespoints;
my $i = 0;
while (<>) {
  my $g = GD::Graph::linespoints->new(100,100);

  $g->set( 
      x_label           => 'X Label',
      y_label           => 'Y label',
      title             => 'Some simple graph',
      y_max_value       => 8,
      y_tick_number     => 8,
      y_label_skip      => 2
  ) or die $g->error;
  my @line = split / /;
  open F,">plot$i.png" or die $!;
  binmode F;
  my $img =  $g->plot(
       [[ 1, 2, 3, 4],
       \@line]
      ) or die $g->error;
  print F $img->png;
  $i++
}
[download]

okay, perhaps you can help me identify the bug using the following file:

Start 

comments

1 2
3 4
5 6
7 8

quotes

End 

Start 

comments

8 7
6 5
4 3
2 1 

quotes

End
[download]

and the following code (excuse the poor quality)

use GD::Graph::linespoints;

my $data_file = "retestfileIN.txt";
open DATA, "$data_file" or die "can't open $data_file $!";
 undef $/;
 $_ = <DATA>;
  close DATA;
$/ = "\n"; 

for my $r (0 .. 1) {
if (/comments(.*?)quotes/sg) { 
    my $tempvar = $1;
    $tempvar=~ s/^\s+|\s+$//g; 
    
    @alltemp = split(/\n/,$tempvar);

    foreach my $line (@alltemp) {
    $line =~ /(\d)\s(.*)/g;
    push(@first, $1);
    push(@second, $2);
    push (@data, ([@first, @second]));
}
}


my $g = GD::Graph::linespoints->new(500,300);  # graph code
  
  $g->set( 
      x_label           => 'X Label',
      y_label           => 'Y label',
      title             => 'Some simple graph',
      y_max_value       => 10,
      y_tick_number     => 8,
      y_label_skip      => 2
  ) or die $g->error;
 
  my $format = $g->export_format;
  open (IMG, ">squot$r.$format") or die $!;
  binmode IMG;
 
  print IMG $g->plot(\@data)->$format();  # end graph code

}
[download]

If I include the code for the graph, the IF never makes it to the second set of data (8 7, 6 5, 4 3, 2 1)

there's my problem

I think the reason that the graph is not quite right is that you are appending to @data on each pass through the loop, but you don't reinitialize it, so on the second pass @data has both sets of data in it. I assume that GD is ignoring the extra set.

I would suggest that you do all of the following as a matter of course:

(1) use warnings;

(2) use strict;

(3) add "my" where needed to declare variables in the correct scope (you won't need to explicitly reinitialize @data if it is made local to the loop), and finally

(4) run the script "perltidy" from the CPAN module Perl::Tidy on your code to fix the indentation. This isn't just esthetic, it can make flaws in scoping and nesting a lot more obvious. (Update: a better description of using command-line perltidy is at http://perltidy.sourceforge.net/.)