Today's transactions are not included in the download, so if you have some transactions going through today that are reflected in your online balance then this may explain why the balance within you personal financial management software package is not the same as the one currently displayed online.
If today's transactions do not explain the difference between the two balances then another cause could be a missing statement transaction. The easiest way to correct this is to perform another download for a period going as far back as when you know the balances matched. Once you have imported the statement download and reconciled the missing transactions the balances should match.
Another possible cause is that you may have manually keyed an incorrect transaction into your software package.