No, the program doesn't know that you have 3 properties, just because you entered 3 1098's. Individuals can have multiple 1098's for different loans on the same property. You will need to remove one of the home's mortgage interest.
You can write off 100 percent of the interest you pay on up to $1.1
million of debt secured by your first and second homes and used to
acquire or improve the properties. (That's a total of $1.1 million of
debt, not $1.1 million on each home.)
As long as the 1st mortgage, HELOC, and second home mortgage are within the limits above, you can deduct the interest.
http://blog.turbotax.intuit.com/tax-deductions-and-credits-2/home/the-tax-benefits-of-home-equity-li...
https://www.irs.gov/publications/p936/ar02.html
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