The "Beginning Statement Balance" on the reconcile window is a calculated value, which is

Initial Balance of the Account+ Cleared Deposits - Cleared Payments

To change the Beginning Statement Balance, you'll need to adjust one of these variables. To change the Initial Balance of the account, open the account register and go to Account->Edit Account.

If you reconciled your account last month and this month you
came to reconcile and the beginning statement balance this month
does not match the ending statement balance from last month there
are a limited number of possible causes.

  1. You modified the amount of a transaction that was already
    marked as cleared.

  2. You deleted a transaction that was already marked as

  3. You manually cleared a transaction in the intervening time.

  4. You deleted a category that contained cleared transactions.
    Deleting a category deletes all transaction that use that

  5. You deleted an account that had transfers to or from the account
    you are reconciling.

  6. Deleting an account will delete all transfers
    that use that account.

  7. You changed the "Initial balance" on the account under
    Account->Edit Account...

  8. You manually marked a cleared transaction as uncleared.

  9. You had the option under Preferences->Network "Mark
    transactions as cleared when confirmed" checked and then performed
    a download and confirmed transactions, automatically clearing those transactions

If you have done any of these things it can be quite tricky to
track down the cause of the change in cleared balance, although clicking the "Uncleared" filter may make it easier to see if you've accidentally uncleared an old transaction. The only way to fix such a problem is to go over the register
and your old back statements and see if you can find anything that
has changed. If the discrepancy is relatively small it might be simpler to
enter a new transaction (Categorize it "reconcile discrepancy") and
clear that transaction.

Some users find it helpful to enter a dummy transaction with a
zero amount and enter a description stating what the cleared
balance was on this date as a marker they can refer back to
later, as in the transaction pictured below.