If your account balance in Cheqbook is different from your balance at the bank, the issue is likely caused by the "Estimated Opening Balance" transaction the system creates for you when you add an account. It is calculated by subtracting the total amount of your transactions from the balance amount we got from the bank.
The "Estimated Opening Balance" will be, by default, the first transaction in each of your accounts and is categorized to blue. You can edit the amount of this transaction to be more accurate or delete it all together. If you add historical data downloaded from your bank prior to this opening balance, you will want to delete this transaction and make a new one at the beginning of your historical data.