I don't know if this will satisfy you or help but there is no requirement or need to enter the rental income through the 1099-MISC. all that does is transfer the amount to schedule E. the 1099-MISC itself is not reported in an e-filing. When you get to the rental properties it will ask about rental income and that's where you would enter the amount from the 1099. schedule E does not indicate whether or not the rent was reported on a 1099.
another thing to try is to delete the 1099s that were pro forma from last year. there could be corruption
if rents you enter on line 1 of the 1099-MISC end up on line 4 of schedule E for just some properties that may indicate corruption in the file. it may be the 1099-MISC or an uncorrectable issue with the file.
