Eugene Boban, has much to do with the history of the crystal skulls. He was a French "Archaeologist", and had several crystal skulls in his collection. Some of the other things he had in his collection turned out to be fakes. Boban had sold a total of 3 skulls to Alphonse Pinart, a French explorer, ethnographer. Many of the first skulls had vertical holes going through them. These may have been actual beads but were then carved into skull shapes by modern people. In 1881, however, a new skull was put on display. This skull had no vertical hole and was life size. Even though he noted this skull as "one of a kind" it did not sell. After a affair with Boban trying to sell the skull to Mexico's national museum, he was exposed as a fraud. He then moved to New York and started to sell antiquities there. The skull was later sold there. Another skull was also recorded but now, neither of these objects are known to exist. More skulls appeared in 1934, one that almost had the exact proportions as a skull the British Museum had bought. It was slightly more detailed and had a separate mandible (apparently very special). The skull is now known as the Mitchell-Hedges Skull.
All skulls have been identified as Aztec, Toltec, Mixtec and maybe Mayan. But these cultures did not represent skulls this way. The first small skull like beads were probably fakes. The other larger skulls may be fakes as well. For all we know the truth of the crystal skulls may have gone to the grave with Eugene Boban.
Picture of the crystal skull is from http://www.archaeology.org/image.php?page=0805/etc/jpegs/indy1.jpg