Long story short, the newer Apple Earpods and simiar do not work with the iPod Shuffle 3rd generation (yet physically they seem the same far as the connectors go), only the 4th generation or newer is supported.
http://apple.com/earphones
Honestly I wish I knew why they did this, all the other non-apple branded earbuds with remotes + mic appear to be compatible with the 3rd generation shuffle (minus the mic capability which obviously doesn't apply), yet the newer Apple one's do not, seems like they're trying to force you to upgrade the shuffle.