HI,
I tried to change the colors of the custom skin in the new version, the result is a bit messy, try it.
I hope this help somehow.
Great job, anyway.

Using the custom theme and modifying the colors in custom.css works just fine. I'm guessing that what you are seeing is that when round corners are enabled, the colors for those don't come through the css. Those are background images out of the graphics folder. To change those, you need to re-color the png images with a graphics editor.