It sounds like your mortgage is being limited. My suggestion is to enter your original 1098, exactly the way it is listed. Combined the remaining two 1098's into one 1098 entry. Make sure in the second 1098 that you record the mortgage balance as 0 since these are refinances of the original mortgage balance amount.
I think this should clear up your original entry. As long as your mortgage balance is below $750K, you should be able to claim all your interest paid in the original loan and the refinanced loans.
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