I to have had this bug.. it also happens to wild chocobos. usually if they go into the water and you walk out of sight.. i had to scrap a really nice map where i was conveniently located near a village, temple, and dungeon. as in they were all on top of each other.. which was amazing! in any case. my problem started when my baby chocobo grew up.. i tried using MCedit to remove the horde.. but.. sadly i apparently missed a few cause when i jumped back in.. they multiplied yet again.. but they were all the wild ones.. my two tame ones only duped on first play.. but they don't move they just float where they are bobbing up and down. funny thing is you can tame the clone and it tames the mobile... any who just my thoughts.