What you can do, is just tell the program that none of the income was reported on a 1099-MISC, and then enter the total rental income received. Besides, that's all that gets reported to the IRS anyway; just the total. The 1099-MISC you enter is not sent to the IRS. Do it my way and check it out.
On the SCH E you will not find anything that indicates how the income was reported to you. All you see is the total rental income received for each property you own on line 3 and that's it. Did it come from a 1099-MISC? Cash? Something else? No way to tell and the IRS could really care less, provided you actually reported the income of course.
