I've been watching (troubleshooting) this since 9/11 and finally figured out that if there are "Pending Transactions" following a download from a lender, and the account is configured to "Reconcile Using Online Balance" it won't automatically reconcile without manually deselecting the pending transactions in that window. Quicken assumes that if the transaction is downloaded, it is cleared even though it is marked a pending. I have a manual workaround, but why are these hotfixes adding to our workload?
Both JP Morgan Chase (Amazon Prime Visa) and First Security Bank of Searcy exhibit this issue.