Yes reconciliation discrepancies can be a bitch to find - under any system.
When you commence the 'reconcile' process QB shows a 'prior reconciled balance' - if this amount is different than the actual reconciliation you did last month then something has changed. But that 'change' may not be a transaction amount - any change to a reconciled entry (even in the notes) can cause it to become 'uncleared', and that changes the 'prior reconciled balance'.
Here one way to fix the problem: start the reconcile process, but put in a date that is one day only after the last reconciliation date, and for the closing balance enter the reconciled balance from last month - and 'hide transactions after the statement date'. Now 'clear' anything that showed as cleared on the last report and 'Reconcile' - this gets you back to square one.
Then start the real next reconciliation.
Still cant find the discrepancy? A reconciled transaction may have deleted, or been redated into the future.