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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