There might be gains or losses from other sources besides the form 1099-B's. For instance, you may have capital gain distributions reported on a form 1099-DIV. You may also have capital losses carried over from a previous year.

What do you mean by the "added 6%"? Are you subject to an excise tax for some reason?

Thanks for the reply Thomas! When recapping income for federal taxes, there's a feature that presumably breaks down your earnings: 

"Your total income of $X comes from adding up your capital gain of $A, the $B of ordinary dividends, your taxable interest of $C, and the $D you earned at your jobs.

Presumably $A is from the 1099-Bs, $B is from 1099-INTs, $C is from 1099-DIVs, and $D is from your W2's. However I've noticed that there's a $5K difference between $A and the total from my 1099-B, and I haven't been able to track that down.

I suggest you look at your form 1040 and schedules 1 to 3, that will list your income by source. You can do that while working on your program online as follows:

1. Find the "Tax Tools" option on your left menu bar and click on it

2. Click on "Tools"

3. Click on "View Tax Summary"

4. On the left menu bar see the option "Preview my 1040" and click on it to view form 1040 and schedule 1 to 3