**Help deciphering JL/AA mileage credit**

So I recently flew JFK-NRT-KUL-NRT-LAX on JL metal, ticketed on AA. AA receipt says "I" class. JL boarding passes say "C". I know about the history of AS codeshare crediting (technically not allowed, but they usually do it if both carriers are partners), so I submit everything to AS for manual credit. I'm MVPG. Week or so later, here's what posts:

JAPAN AIRLINES Flight 62 NRT LAX

Base: 5,451, Bonus: 12,265

Actual miles flown: 5440

JAPAN AIRLINES Flight 723 NRT KUL

Base: 2,838, Bonus 2,838

Actual miles flown: 3350

JAPAN AIRLINES Flight 3 JFK NRT

Base: 5,734, Bonus: 5,734

Actual miles flown: 6730

None of this makes *any* sense to me using any chart. Relevant charts:

JL C: 100% base, 25% COS bonus, 100% additional

JL I: 70% base, 100% additional bonus

AA I: 100% base, 50% COS bonus

Can anyone decipher what's happening here? Or is the support agent just posting random stuff? Only the first flight -- NRT-LAX -- looks even close to correct. The others just seem like random numbers. I'm slightly hesitant to complain because this is technically not allowed, and I don't want to raise flags. Hoping perhaps the wisdom of FlyerTalk has insights. Thanks in advance.