Reconciliation uses different number than entered

In GnuCash the reconciliation feature is available for all accounts, regardless of the account type (whether it's an asset, liability, expense, etc). With some accounts such as a bank savings account, credit card, etc (where you receive statements), there's an obvious benefit associated with reconciliation, because it brings your records into sync with those of the institution. I preface with that information, because while the feature is sometimes needed and is always available, it is definitely not always required or even needed. I have reconciled 'custom' accounts in the past, however I've never considered reconciling an expense account.

In any case, when I open reconciliation for one of my accounts, I see the same windows and fields you posted in your question, with the exception that the "Ending Balance" I enter in the "Reconcile Information" window matches the "Ending Balance" shown and used in calculations on the Reconciliation Window. If I saw a mismatched value like that, I'd probably try restarting the application entirely and see if it behaves better after the restart.