I had a horrible experience trying to get miles credited from an AA flight earlier in the year so I could definitely see that complicating things. Although, if the miles are credited and in you AS account they shouldn't be holding it up. I still think the root cause of my delay last year was the California promotion they did that gave extra EQMs for certain flights but they didn't count towards some perks. Basically, each account had to be manually reviewed. Genius move by AS