I made 3 orders and 2 orders posted at the correct amount. My 3rd order only has $51 out of $127 posted, which represents only 2 of the 7 magazines ordered. I emailed magazines.com and they said:

"Good news! Our records indicate that your order was successfully placed through the appropriate Linkshare. This means that your work is done - simply look forward to your AAdvantage credits, which will be awarded within 6-8 weeks of your order. Furthermore, I see that the correct amount was sent to AAdvantage, so they should be granting points on the full amount."

So, they claim they sent the correct amount to AAdvantageShopping, though I find it hard to believe that it would be posted in separate transactions.