Hi,

While I also am not entirely clear on your problem, I have managed to get your modified code to work simply scoping @temp1 and $domain using my, and by not printing the header out to the same location as the data. The following code generates a PNG image on STDOUT:

#!/usr/bin/perl -w

# Declare the stuff we need to use
use strict;
use CGI;
use GD::Graph::linespoints;

use constant TITLE => "AAA Days to Integration Average: Line Chart";
my $q = new CGI;
my $graph = new GD::Graph::linespoints(600, 300);
my $largestValue = 0;
my (@xAxisOfDates,@yAxisOfPartners,@yAxisOfArf, @data) = ();
#open(HANDLE,"integrate.dat");   # commented out 'cos I'm using DATA
while (<DATA>) {                 # note DATA here
   chomp;
   my @temp1 = split(/\|/, $_);  # use strict needs 'my' here
   my $domain = unpack ("A5", $temp1[17]); # and here
   push (@xAxisOfDates, $temp1[1]);
   push (@yAxisOfPartners, $temp1[4]);
   push (@yAxisOfArf, $temp1[5]);
   if ($temp1[4] > $largestValue){
       $largestValue = $temp1[4];
   }
   if ($temp1[5] > $largestValue){
       $largestValue = $temp1[5];
   }
}
#close(HANDLE);            # using DATA for simplicity here

@data = (\@xAxisOfDates, \@yAxisOfPartners, \@yAxisOfArf);

$graph->set(
   title => TITLE,
   x_label      => "Third Quarter FY 2002",
   y_label      => "Average Days",
   long_ticks   => 1,
   y_max_value  => $largestValue,
   y_min_value  => 0,
   y_tick_number => 10,
   y_label_skip => 0,
   bar_spacing  => 4,
   types        => [ "linespoints", "linespoints" ],
   dclrs        => [ "red", "black" ],
);

$graph->set(
   markers      => [1,1]
);

$graph->set_legend( "Partners", "ARF" );
my $gd_image = $graph->plot( \@data );

# I don't know where you want this, but putting it 
# in the png doesn't seem to work :-P
#print $q->header( -type => "image/png", -expires => "-1d" );  

binmode STDOUT;
print $gd_image->png;
#get_data();   # undefined function; perl not happy

__DATA__
1|1/27|2002|3|26|19|7|7|21|10|3|34|7|73|undef|71|6|20
2|2/03|2002|3|26|19|8|28|21|10|3|34|7|73|undef|72|6|20
3|2/10|2002|3|24|24|8|28|21|10|3|46|7|73|undef|72|8|20
4|2/17|2002|3|22|23|6|28|21|10|3|46|7|73|undef|72|8|20
5|2/24|2002|3|18|23|6|28|22|10|3|46|38|73|undef|72|8|20
6|3/03|2002|3|13|25|6|36|18|28|9|33|38|44|undef|65|8|20
7|3/10|2002|3|13|35|11|50|22|28|9|33|38|44|undef|65|8|20
8|3/18|2002|3|12|33|11|62|24|28|9|33|38|44|undef|65|undef|undef
[download]

Note that I had to turn taint checking off ("Too late for -T option..."). I'm afraid I don't have the time right now to address this issue and must therefore leave it as an exercise for the reader :-)
I hope this answers your problem.

Tim

Update: *sigh*, shows how often I use -T...
This thread explains the taint problem I was having. In short: don't worry about it :-P