I'm not expert (you can see my post on the problems I had), but I think I've learned something useful.
After you soak your wood (for weeks), it's not enough to just scrub it with a brush. Take something (I used a screwdriver) and check for soft stuff. While the soft stuff was there, my wood was still staining the water within a few hours. But after letting it sit in a bucket overnight after scraping all the soft bits off, the water is clear this morning. Maybe the prolonged staining from Mopani wood comes from little bits of softer material that get left behind in knotholes and crevices.