Weird. We had no issue with this.
We managed to stay ahead of the mission goals and avoid all but 1 brown token. And by the end we had 12-13 TU per run.
Yeah that's insane. I am glad you found the right path.
The reason why Madame is horribly balanced is that it doesn't tell players early enough that they should just start over. My group never had more than 5TU and we were constantly punished with further reductions until we ran out of fail cards.
At that point everybody was ready to throw the copy in the garbage bin.