I am reopening this issue because it still exists, and all previous discussions on this topic have been closed, with no clear resolution. The following problem description is copied from a closed discussion from March 2023, entered by user ‘jmich:
Quicken includes pending transactions that it downloads from my checking account in its calculation of the "Online Balance" but it doesn't add the pending transactions to its own ledger. Consequently, Quicken sees a difference between the Online Balance and its own Ending Balance, and pops up a "Reconcile" window which insists that I accept adding a correction to the ledger or that I select "Finish Later". But there is no discrepancy. Quicken should reconcile only the transactions that have cleared and ignore any "pending" (which might change anyway before they clear).