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.
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California does not tax part-year residents on the "full amount" of your federal AGI, unless the income you earned when a non-resident is California source income. You have to fill out California Schedule CA (540NR) and allocate your income and adjustments for the portion that isn't California source. Click the link to see a Schedule CA (540NR).
I can't explain why you're getting different results, but in TurboTax, I recommend you prepare your Pennsylvania state return first, and then prepare your California return. Make sure your filing status for both is Part-Year Resident.
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