I just went through this problem myself and believe I have identified the issue.
The rules appear to be as follows:
If you rent out part of your home for the entire year, when adding your home, the % allocation question appears and Turbo Tax will automatically calculate the values.
If you rent out part of your home for part of the year, the % allocation question never appears and you have to manually calculate expenses & Mortgage Interest on your own and enter the values yourself. This includes manually adjusting Mortgage Interest and property taxes for your personal deduction.
