Even though I have separate groups; when I apply a color to one they both change. What can I do to have them color differently?
You need to provide more information? Are those groups possibly components instead? Are the groups collected together into a larger parent group that you are painting? Share the .skp file so we can see exactly what you are working with and give you an appropriate answer without having to guess at it.
No. They are groups. They show as separate groups. I don’t access to the file at this time but will provide later today.