When corn is delivered to the Cargill facility, it is separated into various parts. The germ is made into oil, the hull is used for animal feed, and the starch is made into a variety of items, including high-fructose corn syrup, corn starch, and ultimately lactic acid, which is made into PLA.
It is technically possible to segregate the corn grown under WLC's sustainable production standards from the other corn going into the Cargill facility, but because of the infrastructure of the massive corn processing facility, it would be very costly to do this--over 30% more--and this would make the packaging too expensive to use. Since the lactic acid and PLA contain no genetic material from the corn, there is no risk of GMO contamination from the packaging to our yogurt.
So, while we can't know for sure whether the corn we contract through Working Landscapes ends up in our cup plastic, we do know that our investment in Working Landscapes certificates ensures that farmers grow an amount of non-GMO corn that's equivalent to the amount of corn we use for our cups. The bottom line is that because of Stonyfield's (and your) purchase of cups made from Ingeo PLA, less GMO corn is grown, and more sustainable agricultural practices are used.