@soyuppy
Since you must be using the downloaded program please switch to the FORMS mode and review the Cap Gains tax worksheet to see exactly how the tax is being calculated. The Cap gains is NOT a separate tax but the income is taxed at different rates after taking calculating the taxable income. May I suggest you print out that worksheet and the form 1040 & Sch 1 & Sch D then get a couple of highlighters to match the same amounts on all of those forms ... it may make better sense that way.
Also you may have some cap gains that are taxed at 0% and some at 15% or maybe 20% so read the form carefully.
