Update: A few days later, I logged back in to TurboTax, and the problem was mysteriously fixed. Maybe I had to sign out for the federal info to propagate fully to the New York return.
My best guess for what might have caused the problem originally was that near the end of doing my taxes, TurboTax said I had missing info and asked for the address of the charity, which they hadn't asked for in the original section for federal itemized deductions. Maybe entering the address caused TurboTax to think it was a cash or some other non-stock donation, so that it could be deducted beyond 30% of AGI? Then when I went back through the federal deductions section, TurboTax remembered that it was a stock donation? And then logging out and logging back in again is what it took for the New York return to also realize it was a stock donation? Just speculating...
