I created several simple ggplot2 plots and saved them to PDF files using the following commands:
p <- ggplot(plotobject, aes(x=Pos, y=Pval),res=300) ggsav
I could solve the problem just by adding alpha specification. If you don't need any transparency you can chose an alpha value of 0.9 ...
example:
ggplot() + geom_point(aes(x=..,y=.., color=...), alpha=0.8)