If you find your accounts are not balancing, try recalculating the balances in Express Accounts to see if it helps. To do this, click the Transactions menu option in the main window and select Recalculate Customers' Balances. Express Accounts will run a recalculation automatically.
Usually, when numbers do not match, it is do to a bad entry. Make sure you have checked all your transactions in the Journal to see if there is something wrong.