Have you tried booking NRT-BKK-NRT on JL's website? You didn't mention if you tried that. I think there are a few issues at play here that can and have happened to others:

1) With partners, aa.com doesn't always have real-time availability info. I have had the same thing happen, also with JL segments. It's frustrating because in some cases it gives the warning when you go to pricing, but in a few cases it doesn't give the warning until you attempt to purchase. At that point you're already set on what they are offering and assume that they have checked availability.

2) Phone agents often don't have access to the cheapest fares. It's worth checking with them, but in most cases you can do better elsewhere.

3) ex-NRT standalone fares are expensive in general, for reasons I don't completely understand. Try pricing TPE-NRT vs. NRT-TPE, or BKK-NRT vs. NRT-BKK someday.

Issue (1) doesn't usually/ever apply to AA codeshares, so that will likely ticket. You could perhaps put that on hold and wait a day to see if any JL availability opens up. You could also gamble and wait longer to see if any JL inventory opens up down the road. I've seen this happen - there are times when I've suspected that JL revenue management consists of a guy in an office with a dart board.

The other alternative is to look into a non-OW partner. As much as I try to stay on OW, there have been too many times lately where I've had to look elsewhere for onwards from NRT because JL was just too darn expensive.