Another player was in Survival mode while using the enchantment table which was placed atop a jukebox, and had an iron axe inserted inside of the enchantment table. We had 14 bookshelves surrounding the enchantment table, and I was in Creative mode placing and removing bookshelves repeatedly to test the amount of bookshelves needed to get a maximum level enchant. As I was placing and removing the bookshelves, the other player was repeatedly inserting and removing their iron axe into the enchantment table. After about five minutes, I set the book shelves back to their initial position, and the other player changed to creative mode and used the same iron axe to break the jukebox. The jukebox broke and we were both kicked out of the server; as soon as we re-joined, the entire chunk that the enchantment table was situated in was re-generated, and the house was destroyed. Additionally, when when entering the chunk that was re-generated, it was raining instead of snowing wherever the player was within the re-generated chunk; if the player moved, the rain would follow the player, and continue snowing where the player previously was.
We were in a Taiga biome on survival. The map was created using the 1.4.6 version of the Minecraft server. In the attachments, the first picture is of the damage, while the second picture is a replication of the enchantment table setup.
I have been unable to replicate this issue.