The Palmerston rider finished first in her final race in Villars-sous-Ecot, France, yesterday but said she was shattered to have placed third overall in the championship.
Starting the weekend in second overall, Duncan held a 15-second lead heading into the last lap of the first race.
However, she was forced to divert to avoid a crash involving five riders on the previous lap, which blocked the hill when Duncan arrived.
That caused her to crash and become stuck in a fence.
She eventually finished in sixth place, but at a jury meeting straight after the race it was decided to award points based on the placings at the start of the last lap. That promoted Duncan to first, but the decision was reversed after legal advice was sought, leaving her with a sixth-place finish.
"It lost me the championship," Duncan told the Otago Daily Times after the final race in France last night.
"I’m very, very devastated but I hold my head high and I gave it my all out there and was able to win and show them what should have been."
Kiara Fontanesi, of Italy, won the championship.
