Solved
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I managed to fix the problem quite easily without getting into a big complicated reconciliation process. I simply reviewed my transactions, found the one that matched the amount it was out (it was already cleared) and selected "undo". Once you do this quickbooks brings it up in your review panel and as non reconciled. Select "match" and it seems to fix it. Now everything is bang on. So it appears quickbooks did not record the transaction even though it said it did when you did it originally. It's like it didn't "take" the first time. A bug perhaps?
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