You may have started reconciling with a current statement, but you didn't reconcile statements of each of the previous months.
You should reconcile one month at a time, starting with the earliest month. If you don't have time for this, allow Quicken to enter an adjustment for you.
You may have inadvertently changed or deleted a transaction that already had an R in the Clr field.
Quicken always asks to confirm a change to a previously reconciled transaction. If you have already ruled out other possible errors, you probably should continue with reconciliation and have Quicken record an adjustment transaction when reconciliation is complete.