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I have the same problem.  If I look at the hard copy 1099 Ally sent, I see a page of instructions after the first two accounts.  The 1099-INTs for the remaining accounts follow the instructions.  The first two accounts are the only ones available for import.  Could it be that Turbo Tax is seeing a page of instructions and assuming that is the end of the 1099 forms?

This worked last year for the same number of accounts.  

I can enter manually but then why did I by TT to download my financial information?