For example, a very flamboyant orange in Prefs, when applied to a state, should make this state be of the same color and also show up on the minimap as the same color, but its hue is actually darker on both.
I wonder if this is a modification quickly introduced to make the background of the transitions attached to this state, and the links departing from this state, be darker too and thus more visible.
A current project I work on doesn't have this problem, even if I'm on 1.8.8f2 now, perhaps because I upgraded from older versions up to 1.8.8 and the Preferences weren't replaced.
But when I make tests by directly installing 1.8.8, the darker hue bug is present.
I haven't moved to 1.9 yet so I cannot tell if this is still there.