Bump this 'cause I've recently bought a Kerrang mag (from Spain) from April 2010. There's an interview with Scott.
Not sure if we already know about this, won't read the 10 pages
So according to Scott the issue is solved. The old contract was renegotiated, they owe Atlantic a "greatest hits" record (by the way it is written, seems it was already released, Buy This?) and a future release of a live album. And they signed a new contract with Atlantic just for "Stone Temple Pilots", of course there's the option, if both parts want, of more records. Scott says "in a year from now we'll seat and see what we're going to do" (about new releases with Atlantic).
So apparently they're out of Atlantic now (if it comes to new music)