I'm also struggling with the same issue. The total miles that the website (and manage my booking) told me I should receive have not been credited. I have made several phone calls and also filled out the on line form (twice). Sometimes I get someone on the phone who promises to follow up, but no follow up. I was expecting 81,500 miles from an early May SIN-MEL-AKL round trip in J, but only obtained 73,500.
I made all screen shots of the booking process and manage my booking pages, as I do since the FLEX/SAVER problems of last year.
I think this could be solved if EK had better IT and what was displayed on the website during the booking process was actually what is in the skywards database (or whatever system they use) as miles to be earned.