No. Your combined deduction between Schedule A and Schedule E should always total the amount reported on form 1098E. If the amount on schedule E is being reported accurately you may have to manually enter the correct amount on the itemized deductions.
Also, you should enter the mortgage interest on schedule E for rental first because it usually automatically carries the unused portion to your itemized deductions. You would not need to enter the amount on Schedule A manually.
But before you do that, please clear your cookies, history and cache' then reboot the computer. Your computer may be caught in a loop.
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