The problem lies in your saying you add the cost of the roof back to the basis. If you entered the roof as a depreciable asset when you put it on, as apparently you did, there is no reason to add it back at full cost as part of basis. The program adds up all the original costs of all your assets to determine the original cost of the entire property. If you add it in again, you're double counting. You could have 20 assets and the program would add the cost of all of them to determine the cost basis before adjusting for depreciation.
