What exactly are you looking at on Schedule D? There is nothing on Schedule D called "total capital gains." What line of Schedule D are you looking at? There could be gains or losses on Schedule D that do not come from Form 1099-B.
And what exactly do you mean by "the 1099 reports"? A consolidated brokerage statement might include several different kinds of 1099 forms, such as 1099-INT, 1099-DIV, 1099-B, 1099-OID, and 1099-MISC. They do not all go to Schedule D. Also, your 1099-B forms could include losses as well as gains.
A typical consolidated brokerage statement shows net gain or loss for each category, but each category is shown separately on Schedule D. You can't just add them all together. And Form 1099-B itself does not show gain or loss. It shows only cost and proceeds. The gain or loss is calculated on your tax return. The gain or loss shown on the brokerage statement is additional information provided by the financial institution, but technically it is not part of Form 1099-B.
You have to be precise about exactly what figures you are looking at on the brokerage statements, and what lines of Schedule D you are comparing them to.
