I'm just guessing here, and I've got two guesses
Quess 1: It "sounds" to me like you entered the 1098 for Home 1 twice. Once in the rental section you entered the total amount in box 1 of the 1098, and again in the Deductions and credits section you entered the total amount in box 1 of the 1098.
If in the rental section you elected to have the program do the split between SCH E for the period of time it was a rental, and SCH A for the period of time it was personal use, then you do *not* enter that 1098 for Home 1 anywhere else in the program. The program (not you) will do that split between SCH E and SCH A.
Guess 2: You indicate you have a total of 3 1098's. I'm assuming one is for the rental. The other two are for Home 2, and you have two 1098's for home 2 because the lender sold your mortgage to another. I would not be surprised if the 2nd 1098 from the buyer of that mortgage also included the interest already indicated from the 1st 1098 from the original lender. You can check that by logging on to the website of the lender and looking at your payment history. Add up all the interest payments and they "should" equal what is shown on that 2nd 1098. If they are less than what's shown on that 2nd 1098, then the buyer of your mortgage may have incorrectly included your interest payments to the original lender.
