Japanese culture is different from the United States or Europe.
The plane crashed. It was a JAL plane. Therefore JAL and its executives are responsible for those deaths, and JAL pays some money for expenses related to those deaths and suffering of the survivors.
This money is not an admission of liability, or guilt, or responsibility on the part of JAL.
When I arrived in Japan in 1982, one of the briefings on the cultural differences included this example. If I'm stopped at a red light and a following driver fails to stop and rams into my car - if that driver or any of his passengers are injured - I will visit them in the hospital - give them a few thousand Yen - and express my sorry to the personally that they were injured in an accident that I was also involved in. That expression of regret that anyone was injured in no way impacts my claims against that driver or his insurance company for damages, compensation for loss of use of my vehicle or my pain and suffering.
It cannot be used against me in court as an admission of guilt - as it would in the US or most European countries.
The 780 million Yen was just that. Nothing more.
At current exchange rates - 780 million Yen is about 9.86 million USD. At the time of the crash my memory is that the yen/dollar exchange rate made the 780 million Yen worth about 6.5 million USD - or about $12,500 per fatality.
The Wiki article on this crash is filled with errors. It is frequently edited as various groups try to shift the blame on others and hide the massive culpability of the Tokyo Metropolitan Police Department in the failure to initiate a prompt rescue effort that would have saved several lives.
I was stationed at Yokosuka at the time. I was over the crash site in one of almost a dozen US military helicopters that night. I was on the ground at the crash site before noon the next day.
The initial PR
campaign by JAL to blame the flight crew for not landing safely at Yokota failed miserably as simulator reenactments were unable to find a way to keep the plane in the air.
By the time I left in Japan in November 1986, the local papers were reporting several lawsuits filed in the United States against Boeing and JAL by the crash survivors and families of the deceased.
My understanding is that Boeing, JAL and the Tokyo Metropolitan Police Department (they had jurisdiction over the crash location and responsibility for oversight of SAR) - all settled out of court. That no cases actually went to a jury, and that all amounts paid were sealed.
Part of the Boeing 'compensation' was reported locally as a replacement B747 aircraft for JAL. I have no idea if that actually happened.
But to answer your basic question - Yes, Boeing did pay several million after the crash. How much and exactly how the legal papers were worded will probably never be publicly known.
[Edited 2012-06-06 06:06:18]