I don't know how to ask this question, maybe others have some insight...I moved mid-year from California to Pennsylvania, and I am filing in both states this year. For some reason, the Turbotax calculated CA tax, given my reported CA AGI, is about 40% higher than the amount given by other estimated tax software or even CA-FTB's free site. (Filing with FTB is really tricky because it doesn't give an opportunity to split reported Federal AGI across states--it taxes you for the full amount). Some of the income (~20%) is from scholarship stipends and I have a very small penalty, but it's otherwise included in the AGI so I don't know why the tax amount would be different from one site to another. I don't know if that has been the case for anyone else.
