The Atlantic story I've read in several books on soul music & the Memphis music scene. Apparently, the Stax people thought they had a purely distribution deal with Atlantic, but buried somewhere in the contract (and apparently Jerry Wexler may be one of the guilty parties) was a clause that gave Atlantic ownership of the masters. I don't know the technicalities, but I think this came to a head when Warner bought Atlantic, and Atlantic ended up owning all the pre-1968 Stax masters, which is why all those Otis Redding albums are on Atlantic.
I'm pretty sure it's all covered in Peter Guralnick's excellent Sweet Soul Music.