ATV owned what had been under the Northern Songs banner back in the day. Anything from 1968 or so was published under Apple and not part of ATV. The Beatles or their heirs still own that publishing AFAIK. The acrimony over the ATV publishing stems from when it was being sold in the 80's. I'm going from memory and don't want to look it up but from what I remember, ATV's owner approached Paul first and offered him first refusal at a far lower price than what Jackson ultimately paid. Paul approached Yoko, ready to do the deal with her as partner. Yoko, knowing that John's death would allow her to claim his share eventually, told Paul it was too much money and I think persuaded him to try and deal. Jackson, awash in Thriller cash at the time, swooped in and seized the opportunity, having learned from Paul that "Publishing is where the money is". And Uwe, you are exactly right about Paul's other holdings. He got beat at his own game and I have a hard time working up any grief over that fact.
I've sadly learned the hard way that money has a way of flowing to those most responsible in their stewardship over it. Jackson's irresponsibility in insisting on living a lifestyle he could not afford led to him losing that publishing and everything else. He 'owned' the Beatles publishing in name only. Sony, BofA and many others have owned a claim on those holdings for a while now. He's almost lost them outright a few times when he couldn't make payments on his loans. He (or his people) seemed able to save them each time, but always by leveraging those holdings even further. He's reported to be in debt $400 million or more. I'm not sure that the resultant uptick in MJ sales (though it will be large) is going to cover $400,000 by the time everyone's fingers are out of the pie.
I do feel sorry for his kids though. Unless one of MJ's family or hangers-on can figure out a way to make a buck off those kids, they'll end up with nothing...