Same situation here. I'm guessing that you listed CA as your State of Residence. I did this and could not manage to get TurboTax to even offer the option of filing 540NR (non-resident). I finally got the software working, by doing the following:
On the "Personal Information" tab, I answered the State of Residency question as "Foreign Territory or U.S. Possession". Then in the "Other State Income" section, I listed California. This triggered TurboTax to include the CA state taxes. In the State Taxes tab, TurboTax will ask all the appropriate questions to determine if you need 540 or 540NR.
Good luck!
