As I see it, things appear to me that the program just flat out can not correctly handle your situation. Another thing to, is you "seem" to indicate that you did have at least one full tax year where the property was never rented, or even advertised for rent. If so, the correct thing would have been to convert the property back to personal use. When converted back to rental again, you'd start depreciation all over from year 1 using the adjusted cost basis of the structure only, to account for depreciation already taken in prior years when it was a rental.
