In the arrange window, you can assign colors to regions, but not to tracks per se ... and that's probably the issue here. In the Track mixer, you are assigning color to the track strip, but in the arrange window, to the objects in the track ... they are different things.
Personally, I find myself wondering why the object icons are not displayed on the track strip in the track mixer ... that would be a good way to tag the tracks.
One good thing is that the two windows are linked, so when you select a track in one, it automatically selects in the other .... not sure if that helps.
