Yes, this is a known issue. It's documented in the Release Notes in the :Known issues and limitation" section.
"Coloring does not work for alternative dimensions in Qlik Sense 3.1 and later. The color is grayed out.".
I don't have any information as to why this limitation exists or if it will be removed. Perhaps someone from Qlik will chime in?
Hi Matt & Rob,
This is actually a bug and will be fixed for the September release. When you use auto it should just work.
The limitation we have is that if you create a visualization and then set it to color by a dimension you color it by the dimension that is set. Then when you switch to an alternative dimension you are still coloring by the previous dimension that is still set. Which is why it can turn gray.
We are working on adding an option to color by the currently used dimension.