The two different versions have slightly different sets of letter tiles. The Wooden Box "Bookshelf" edition has 32 tiles, while the Discovery edition has 28. Twenty-five of the tiles appear in both sets, and there are a total of 35 distinct tiles between the two sets.
The Bookshelf edition appears to have some tougher letters, like W, X, Z, that the Discovery version does not have. Also, the font used for the Bookshelf edition is much larger than the one used for the Discovery edition, which may make it easier for some players to see during play.