I narrowly missed out on requalifying for MVP in 2008 because of 4 TATL flights that were some mix of AF/KL/NW codeshares/metal. A year without any status, upgrades, and ~40k RDM eventually missed as a result. It was embittering. At the time I didn't understand the rules, was too busy to follow up, and thought mailing in the BPs wouldn't have changed anything. Last year my girlfriend got EQM credit for a partner ticketed codeshare flight that wasn't technically eligible. She just called, didn't even mail in the BP- sounds like it's always worth it to ask.

I didn't swear off AS cuz I fly out of FAI and have little choice, but I'm guessing that more than a few leisure FFers have had similar experiences where they bought tickets on partner airlines they thought were eligible for credit, didn't go to the same lengths that FTers do to ensure eligibility, found themselves without their FF rewards, grumbled, and took there business elsewhere next time. AS may not lose business upfront and they'll save money by not giving any miles to passengers on these flights, but I bet they lose loyalty by having these subtle holes and seemingly arcane complexities to their program.