I'm confused - you did try the logical thing of doing this twice - once for the 2 sets of x-vals and once for the 2 sets of y-vals?

I haven't yet used GD::Graph, but the syntax you gave seems to imply that

my @graph_data = (\@x_vals, \@y_vals)
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is the expected format. So...

@x_vals = (@x_vals1, @x_vals2);
@y_vals = (@y_vals1, @y_vals2);
my @graph_data = (\@x_vals, \@y_vals);
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If this isn't the solution, then you'll have to wait for someone who knows perl and/or GD::Graph better than me...