The cost or other basis reported on your 1099-B is the value of the stocks on the date they vested. From that day on, if the stock increases in value, you will be taxed on capital gains when you sell it.
Usually on a sell to cover, the stocks are sold as soon as they are vested so there would not be a capital gain. But yes, if the stocks were held and the sell to cover was not executed for several weeks after they vested, you do pay capital gains on the difference between the sale date and the vesting date. Of course, if they went up in value in that time, there would also be more taxes withheld from the sale which would more than cover the capital gains.
