I've placed all the beans into the bowls in Munkarama according to the layout described in the cluebook. When I pull the spindle it keeps coming up White, White, White, White instead of all Black...

What went wrong?

If I've saved since placing the beans, am I now just screwed as I cannot redo them?

There is some randomness to the puzzle. IIRC the solution in the cluebook is only one of the possible ones.
Also, you can pick up the beans again and redo the puzzle.