A possible cause for the issue can be MATLAB switiching the auto-renderer setting to '-opengl' to render the plot. This generally happens when the number of elements exceed a certain threshold in the figure.
The workaround is to manually force the '-vector' renderer, this should give correct graphics output. You can try adding the following command to the script and observe the results:
print(hfig,'-vector','-dpdf',[fname,'.pdf'])
