Enclosed a couple of code snippets from a stat. program I currently have in production, that might help you.
You have to explicitly calculate the Y min and max from your data sets, and then set the graph y_min_value and y_max_value options accordingly to scale the graph.

<more> You may chose to do this in a plot 'wrapper' function.

### ======================================================
### UTIL: plot (using GD::Graph::$type)
### ======================================================
sub plot {
    
    ### Set options for graph, cf params and default
    my ($rOpt, $rData, $type, $x, $y) = @_;     # %Opt, @data, ...
    $type ||= 'hb';                             # Default horiz. bars
    $x ||= max(scalar(@{$rData->[1]})*20, 150); # Scale to num. data.p
+ts
    $y ||= 400;                                 # Fixed (dyn: max(ceil
+($s/2), 400);)
     
    my @opt = %{$rOpt};                         # Flatten option hash 
+to array
    my $graph;                                  # (width:y, height:x)
    if ($type eq 'lp') { $graph = GD::Graph::linespoints->new($y, $x);
+ }
    if ($type eq 'hb') { $graph = GD::Graph::hbars->new($y, $x); }
    $graph->set_x_axis_font(gdTinyFont);
    $graph->set(logo            => ".\\KMD.gif",
                logo_resize     => 0.5,
                logo_position   => "LL",    );
    $graph->set(@opt) or die $graph->error;
    
    
    ### Plot graph, cf @$rData array
    my $gd = $graph->plot($rData) or die $graph->error;
    my $dir = Win32::GetCwd() . "\\plot";
    unless (-e $dir and -d $dir) { mkdir($dir) or die "can't mkdir $di
+r: $!"; }
    open(IMG, ">$dir\\$rOpt->{title}.png") or die "can't open $dir\\$t
+.png: $!";
    binmode IMG;
    print IMG $gd->png;
}
[download]

Example of calling the plot util function:

### ------------------------------------------------------
### Plot SDPI-$y-$mm-Load-($avg[0],$avg[1])
my $max = max(@{$data[1]},@{$data[2]});     # max val. data pt.
$avg[0] = sum(@{$data[1]})/scalar(@{$data[1]});
$avg[1] = sum(@{$data[2]})/scalar(@{$data[2]});
$avg    = sprintf( "%.1f,%.1f", $avg[0],$avg[1] );
my %opt = (
    title           => "SDPI-$y-$month[0][$m]-Load-($avg)",
    x_label         => "Hour / Day",
    y_label         => 'Forms/Min: Avg.(green) & Max(red)',
    y_min_value     => 0,
    y_max_value     => $max+1,              #ceil($max + $max*0.1),
    y_tick_number   => $max+1,
    y_number_format => "%3d",
    two_axes        => 1,
    show_values     => 1,
    values_vertical => 1,
    values_space    => 8,
 );
plot(\%opt, \@data, 'lp', 400);             # Float
$opt{title} .= '-';                         # Fixed
$opt{y_max_value} = $opt{y_tick_number} = 40;
plot(\%opt, \@data, 'lp', 400);
[download]

</more> Best regards
allan