i have the same problem with online missin miles claim.
the best way to claim its to send an email to:

[email protected] (if you're gold)
[email protected] (if you're silver)
on the email subject you put "Retro Credit"
give the you're ticket number and your booking reference + your missing miles flight
its the easiest way and the fastest to claim your missing miles and to get your miles credited.
the managing director of an emirates office tell me that and it work perfectly.