Did you find the solution?
I just ran into this problem too. A family I added to my tree on ancestry now have several children with gender unknown. I couldn't fix it in FTM.
Fixing the gender on my tree in ancestry, then syncing doesn't fix it.
Ok, what seems to have worked for me was:
In ancestry, fix the "sex" of problem people
In the FTM: go into profile, I now had multiple sex/gender facts for each problem person
Change the preferred fact to one of the other entries
Delete all other Sex facts.
The problem appears to be resolved.