As you're reconciling you may find a transaction that appears on your paper statement, but not in Quicken. Here's how to add that transaction to Quicken:
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In the Reconcile window, click New. Quicken will switch to the account register and select the new transaction line.
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Enter the transaction as usual.
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Click Save.
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Select the Return to Reconcile button on the top right of the register (below the gear icon). Quicken will reopen the Reconcile window.
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Mark the transaction cleared.
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Continue reconciling.