from what you've mentioned - it sounds like the agent screwed up. they quoted and charged you for the fare which was correct at the time, but may not have taken into account that CX has just increased fares, mainly for F & J.

Let me ask you...are you holding an e-ticket for your journey? If so, just call CX or MPO and re-confirm the ticket is valid to travel and forget about the travel agent's $200 fee.