I'm surprised Minecraft didn't crash outright. Single Player Commands doesn't have a 1.4.2 version yet. Also you can play offline as long as you've had a successful login before.
@Nikita: It's been present for a while. Minecarts have the same behavior, albeit one block lower visually.
Are you trying to report something for Minecraft Pocket Edition? This is the tracker for the desktop version. Also you need to supply more information.
In the first screenshot, the temple is actually in 2 biomes: River & Jungle. Poking around inside, it seemed to have been actually spawned the river biome. I'd look around the Swamp one and see if there is a river there as well. I have a hunch the temple spawn generation is seeing rivers as a valid desert to place them.
Something I noticed. The oak fence type is not grouped with the other fence types, instead it's up with the silverfish blocks.