We have run into this problem as well, everything appears to be drawn correctly, no gaps, right heights, etc but still persists.
This appears to be based on the Renovation Status of the zone itself. If the zone has an existing status it will ignore walls with a new status. Once the zone is changed to new, it recognizes the boundaries created by new walls (or other boundary objects). Don't know if that is documented anywhere, we stumbled across the solution.
kevin s burns, AIA
massachusetts, usa
AC25 (1413), since AC6
Windows 10
Intel Core i7 -8700 @ 3.2 GHz~ 16 GB ram