GNUPlot is able to generate graphs in SVG, however when I run the html file that references it through prince it ignores the color of the marks on the graph (they should be red).

perhaps prince does not support the "currentColor" keyword?

the svg file can be found here: http://www.alexmac.cc/gnuplot.svg

I've included a sample html file, try it out using:

prince http://www.alexmac.cc/gnuplot.html

This appears to be a bug in the handling of currentColor in SVG when there is a color attribute on the same element. We will fix this for the next maintenance release. Thanks for letting us know!

Today we have released Prince 6.0 rev 5, which fixes this issue affecting the CurrentColor keyword in SVG.