When the statement has a C in the reconciled field, this means that you have matched the transactions together in the statement, but haven't actually committed the reconciliation to the nominal transactions.
To commit the transactions
Click the Update Reconciliation button in the statement window. This can be found at the top of the window in the centre, it has a Floppy Disk with a cog wheel icon.
When you have clicked this, it will you to confirm that you want to update the reconciled transactions.
Click Yes and this will then update the reconciled status in the nominal transactions window.