Get your taxes done using TurboTax

from 1116 instructions

For lines 3d and 3e, gross income
means the total of your gross receipts
(reduced by cost of goods sold), total
capital and ordinary gains (before
subtracting any losses), and all other
income (before subtracting any
deductions).

you'll have an issue if you use the summary boxes on form 1099-B for types A or D capital gains.  because they are  just a total summary of all transactions of each type (no detail of gains vs losses) TurbtaxTax will not be able to exclude losses included in these boxes.