In general, if you are spreading out points over the life of the loan, I would calculate them from your own records and enter them manually. I don't always trust the assumptions that Turbotax makes.
That being said, I do think the program should ask you if you are spreading out points (amortizing) or claiming them all at once, and it should ask you for the date of the mortgage. (In fact, the origination date and points paid are both on the 1098.) So if the program wants to deduct all the points this year instead of just 12/360s of the points, double check your answers, but you may need to call support.
