From Minecraft Wiki
September 13, 2013
1.6.3-pre is the pre-release for 1.6.4. It was released to provide a fix to allow structures to be saved with the world file.
2 bugs fixed
- Structures (witch huts, nether fortresses etc.) don't get saved with the world file
- In order for current structures (Witch Huts, Nether Fortresses, etc.) to be saved to the world file, the player must load the appropriate chunks within the game manually. The game will not automatically scan worlds and update structure data globally. After this is completed, structures will be compatible in all snapshots starting at Snapshot 13w37b
- Fixed handshake exploit
- 1.6.3 was reuploaded. The first was released alongside 13w37b on September 13, and the second one was released on September 17. The first one cannot be downloaded from any official source anymore, although the second one can be downloaded from Mojang's servers. Opening this jar as an archive reveals the file modification dates to be September 17, contradicting the announcement made on September 13. This proves that two versions of the same version number were released.