Can you provide a screenshot of the colors you use in encore for your color set? And when you build the blu-ray disc, do you preview it in a software program like PowerDVD? Or do you burn it to a disc and use your hardware blu-ray player?
Here's a screenshot of the color set. I created a new color set, called it 'Color Set', and changed the selected and activated states of highlight group 1. The selected state is white (255,255,255) with an opacity of 40%. The activated state is black (0,0,0) with an opacity of 20%. I tried variations of white and black that were not so extreme (220, 220, 220 and 35, 35, 35 for example) but had exactly the same problem - the selected highlight, instead of being white, comes out gray. This problem is just on blu-ray, if I output to DVD it works fine.
I having been using PowerDVD to play the blu-ray. I tried burning it to a disc and using a hardware blu-ray player - it had the exact same problem.