I have a similar problem with 2002. When I get my statement and enter the transactions, the balance is always off. This is because the statement date is a little later than the period the statement covers so the prices may be a little different. Also, some of the accounts show what is called accrued dividends. These dividends are from the end of the statement period to the actual date of the statement. Check if your downloads have something similar happening to them.
John