Haven't seen anything listed, but I would bet that they somehow "fingerprint" their media, and then use something akin to Shazam to see if a given soundtrack can be matched against the fingerprints in their catalogue.
The real issue here is how do you handle Copyright for "naturally occurring sounds" (Birds, Waves, Wind through Trees)? Chances are someone produced a library of these things for license. Do they hold the copyright and are they allowed to license their library? I'd say sure. They produced it with (presumably work on their part).
Okay, now someone else (as in our story), goes out and produces an all new original recording of the same naturally occurring phenomena. Why should the new person not have the copyright for their new work? How do you prove actual infringement?
The only way I can think of is that in order to prove copyright for naturally occurring sounds, there must be some acoustic signature inserted so that they are no longer naturally occurring sounds.
Its akin to me taking a picture of the skyline and using it on a web page, and then being sued because someone else already took a picture of that skyline and had it in a database somewhere.