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.