I have similar situation, I got three 1098 forms as I did two refinancing on my primary home.
Two of them have Box#7 unchecked and the Third has Box#7 checked.
For the third 1098 entry in TT I tried entering with Box#7 checked and unchecked there is a $100 difference in the tax I owe to state (CA). Looks like the tax treatment by TT is not the same for box checked vs unchecked.
Please clarify
