Bank account - cleared items not reconciled

This problem is starting to happen regularly: When I reconcile my bank account, there are Cleared items that do not show up in the list of Payments and Checks. So the account does not reconcile. I went back to mark the as (R), but the account still does not reconcile. I have Validated and Super Validated. The specific payments are at the beginning of the statement month or at the end.
I don't mind manually reconciling the missing payments - I have done that in the past - but it is not working now.
Any ideas of what to try next?