This is not a "disaster", that is exactly the way the program is intended to work. Flight Points are a marketing device which allows you to earn one extra point per dollar of spending.
I had to spend an hour gathering documentation of my CX flight, writing a cover letter, and sending this to Citi in South Dakota; it seemed like a great waste of time. My second CX trip still hasn't been credited, so I i will likely have to do this again.