You need to specify the axes to plot against in the dataset object. Having no idea what your code or data looks like, the following example should help. Note, I'm on Windows 7 x64 / Strawberry 5.18.1 MSWin32-x64-multi-thread, so the 'gnuplot' and 'terminal' arguments are required to the chart object to get it to work.

use strict;
use warnings;
use Chart::Gnuplot;

my $chart = Chart::Gnuplot->new(
    gnuplot => 'C:\usr\bin\gnuplot.bat',
    terminal => 'wxt',
    yrange => [0,5],
    ylabel => 'Primary 1-4',
    y2range => [0,50],
    y2label => 'Secondary 10-40',
    y2tics => [0, 10, 20, 30, 40, 50]
);

my $dataset1 = Chart::Gnuplot::DataSet->new(
    ydata => [1,2,3,4]
);
my $dataset2 = Chart::Gnuplot::DataSet->new(
    ydata => [11,21,31,41],
    axes => 'x1y2'
);

$chart->plot2d($dataset1, $dataset2);
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