When did you book your Sept and Dec flights?
What I suspect is that your original WT+ fares for your Sept and Dec flights actually booked you into Y or J class, which was then economy, but since the introduction of Club Europe, you have automatically been put into CE on those flights - this is irrespective of your long-haul upgrade.
The agent is right that if you want to upgrade to CE on domestic, the extra 3,750/4,500 (off-peak/peak) is chargeable because each upgrade sector is charged individually. This is different to full reward bookings where domestic connections are thrown in for free.