I have one product that comes in 12 colors and 4 sizes of each color. The problem is it comes in navy blue and royal blue. The color for each of these is listed as blue, to make our layered navigation easier for the customer to use. In doing so magento won't let me attach both colors to the configurable. If I use a third option for color swatch when creating a configurable there are 3 dropdowns on the buy page where there should be 2. If I use color swatch/size to create, then the layered navigation doesn't work.
Is there another solution, maybe to make the configurables not require a unique value for color?