You are reporting the sale in the rental section, right? You are going through each "asset", indicate it is sold, and then enter the sale price, right?
If so, the program is SUPPOSED to ask you if it was your main home, and answering yes to that will prompt the questions about the exclusion. If it is not doing that, sometimes this early in the year there are glitches that cause the program to miss questions, so you may need to wait a few weeks and try again.
But you are right, in your case you should only be paying tax on the gain due to the depreciation.
