You should try to make sure that your Bonus number is in your PNR and shows up on your Boarding Pass (not all bp's are formatted to show them, but in many cases they are)
Having the miles automatically post is of course the way to go - manually sending them in is an uphill battle, as you found out.
Their level of organization leaves a lot to be desired.
A lot.
Having said that try posting a question on their forum (
http://www.aeroflotbonus.ru/board.as...BoardId=271365) but be prepared that you may get a variation of "we never got em', please resend, please re-fax, etc etc"