I've used Jira's Agile board to color code my epics. When those epics are included in a structure hierarchy, the background color is as I set it in the Agile board. However the link text itself is blue (not white), making it impossible to read unless the background is light. Previously epic link text in the Structure display was white. I have NO idea what happened. The epic name's text still appears white when looking at the epics in the Agile board.
Here is an example of the blue text, which is difficult to read against almost all the backgrounds.
7-22-2015 4-32-16 PM.png
But the text looks fine on issue pages for issues that are part of the epic:
7-22-2015 4-50-51 PM.png
And the text is fine in the agile board, which is where I'm assigning which background color to each epic:
7-22-2015 5-02-38 PM.png