Not all the color options are showing up in the layered navigation. I probably have 10 color options listed in these items, but the layered navigation is only showing 2, 5, or 6 (depending on which category I'm in). I know that number will change depending on the category, but it isn't reflecting the actual colors that are available in that category. Many are missing.
This example is only showing Dark Heather and Sport Grey in the layered navigation. But the 4 items listed also have the following color options available: Black, Royal, Carolina Blue, Charcoal, and Navy.
Have you performed a full re-index and cache refresh?
Yes, I flushed everything: