I had the same problem a couple of days ago while trying to book DFW->NRT->HKG and PVG->LAX->DFW. Multi-city search based on price showed exactly what I wanted but became unavailable at the last possible moment, as in after going through all the credit card details and clicking the Finish button. This behavior was consistent and repeatable over several attempts. I finally solved the issue by switching to a search by schedule. However, the fare did end up being $100 more per person. Talking to web services about it, the problem appeared to be with the NRT->HKG segment which was originally showing as a CX codeshare on a JL flight but which only appeared to be bookable as a true JL flight number.