Well, I use Acros and HC-110 and Ilford Rapid Fixer. I wouldn't say that the fixer comes out 'dark.' I would say that it comes out pink. Anyway, this color DOES disappear by the next time I develop film. I have no idea what is going on exactly. Maybe the iodine is fixed out, and then exposure to light kills it?
The rinse also comes out pink. Since I don't save this water like I save fixer, I can't say if this color will disappear over time? Maybe I'll save a cup of it one day and see what happens.
Anyway, I've found that TIME is the one solution to getting rid of the pink. I do 6 water rinses- pouring water into the tank, letting it sit, pour out and replace with fresh. I've found that the longer I wait between changing the water, the 'quicker' the pink goes away. So if I rush three rinses in five minutes OR I do one rinse in five minutes, it seems I end up with a similar level of pink remaining. So I do my 6 rinses over 20-30 minutes, letting the water sit longer each round (well, the first two rounds are 10 and 20 agitations, then dump, so I can look at the negatives without dripping bright pink everywhere).
I've tried hypo-clear, one common answer I've seen. Now it TURNS PINK and STAYS PINK! Weird.... Well, I gave up using it to reduce the number of chemicals I need around, and my film is not pink by the end of my washing.