One thing I question is just "how" you are reporting this rental on SCH E. Are you reporting the rental unit as a physically separate item on the SCH E? Or did you select the option for "duplex and I live in one of the units."?
In other words, if you're reporting the rental unit as it's own separate entity, then you are claiming 100% of the expenses that apply to that entity. Whereas if you're reporting it as "a duplex and I live in one of the units" then either you are entering 100% of your expenses for the entire structure and the program is applying 50% of those expenses to the SCH E. Or you are doing the math manually and entering the actual costs for the rental side only, as 100% of those costs apply to the rental.
