If you can see the booking on JAL's website but not the JAL flights, then call up AA and ask if there's something screwed up in the reservation. Otherwise, you should be able to see those flights there.

I'm on the same route with the same issue. AA shows no seat assignment online, but it showed they assigned me 47A outbound/47K return on the email confirmation. I'm not a huge window seat fan and would rather have the aisle seat next to it (or preferably somewhere closer to 27). Calling AA didn't get me anywhere either.

Steps are pretty simple:

1. call AA and ask for JAL record locator
2. go to JAL's american reigion website
3. go to "view my reservations"
4. enter JAL record locator number and your details
5. edit there.

I got into my reservation JAL website
Shows no seats available but confirmed economy plus
So do they not come available until the 72 hour prior window?
Can I call JAL?

The problem is that the JL segments aren't showing up at all on the JL site when the flights are AA codeshare flights. I can see my AA flights just fine on the JL site using the JL locator, just not the JL flights.

They may just be blocked, and then become available at 72 hours for OLCI. But you can try to give JAL a call, and see what they can do.

This is AA codeshare. He will need to talk to AA not JAL.

Yes, sorry my thinking was not quite there it seems.

In my experience, the "manage my booking" feature differs between the JAL US site and the JAL JP site.

For my upcoming flight, I can only see my partial reservation with just my US legs on the JAL US site, however, when I switched to JAL JP, I can see the full trip

So for those who are having trouble seeing your JL operated flights, change the website region to Japan, English and look for the "My International Booking" link

AA site for checkin codeshares JL flight
 

I broke a BOS-SYD, SYD-LAX ticket and was issued a AA codeshare JL metal for BOS-NRT on JL7/AA7375 and a JL 771 for NRT-SYD, and AA 73 for SYD-LAX. I used the JAL site and JL record locator and could only see my JL flight to choose seat. At 72 hr, I could check in the JL flight, I decided to call JL. The phone rep told me to go through AA and I replied that I had already done that on AA and I could only see the AA flight when I check. however, she told me to use the check in button at the top left of the screen, and lo and behold, when I clicked on it,I got moved to the same JL checkin site, but this time, the JL7 flight appeared as well and I was able to checkin and issue the boarding pass. I thought I knew but this is great.

Had issues JAL & AA assigning a seat for me, after a few calls was told that AA codeshares booked in class G,N,O are ineligible for advance seat assignments even with status.

On my most recent trip booked as AA codeshare, AA's link to OLCI finally worked.

Trying the old way (get JAL PNR, go to JAL's OLCI, input info there) had never worked for me.

Once in to the JAL OLCI, you can work part-way through the process, get to seat selection, and once selected, drop without completing OLCI (if you don't want to - I figure I'll be at the business class counter at the airport anyway). JAL will save your seat selection.

This also allowed immediate seat selection for the return leg even though that was far more than 72 hours away.

Everytime I have flied JL metal on AA codeshare, I have tried using the JL PNR but the only legs that show up on the JL website are the AA metal ones.
Any suggestions?

Here is what I got returned when trying to pre-assign a seat
Please note that there are some restrictions because the reservation made by other than JAL' reservation system.
It might not be updated.
It might not be shown all.
Unable to assign or change your seats through JAL home page.
Please ask your travel agents or airlines you asked.
If you made the reservation on other than JAL home page at Japan region, please call JMB award reservations and services.

Since I am in "O" class I assumed that the above was the case. I did however think that PLT status would have given me some benefit :D

Unlike CX, fare rules trump status in this case.