Plotyy right y-axis and associated data shifting upwards when enlarging the figure

Question

I used code similar to the plotyy function to plot two y variables. However, the righthand side of the graph containing the second y-axis shifts/moves when I alter the size of the figure. This also results in an upward shift in the y variable from the bottom x-axis. This doesn't happen with the left y-axis. How do I lock/prevent the right y-axis and its associated y variable from shifting upwards, away from the base of the x-axis?

%Some code

hFig=figure;

%Line 1 (blue line variable)
hl1 = line(x1,y1,'Color',deepskyblue,'LineStyle','-.');
ax1 = gca;
set(ax1,'LineStyle',line_style,'FontSize',axis_font,'XColor',x_color,'YColor',y_color);

%Line 2 (black line variable)
ax2 = axes('Position',get(ax1,'Position'),...
           'XAxisLocation','top',...
           'YAxisLocation','right',...
           'Color','none',...
           'XColor',x_color,'YColor',y_color);
hl2 = line(x2,y2,'Color','k');
set(ax2,'LineStyle',line_style,'FontSize',axis_font,'XColor',x_color,'YColor',y_color,'XTick',[]);
linkaxes([ax1 ax2],'x'); %Links the two x axes

%Save figure 
set(hFig,'Units','inches','Position',[1 1 12 6]); %[x y width height]
saveas = input('enter the filename to save as an image','s');
print(saveas,'-dpng','-r300');

Original plot (Note: The original figure was saved manually in Matlab):

After resize (Note: The after resize figure was saved using the code below. This is where we see a shift in the right y-axis):