Couldn't find this bug in the list. Sorry if it's a duplicate...
Create a superflat world (redstone ready)
setspawn at 56 56 56 (/spawnpoint @a 56 56 56)
/kill
set new spawn (/spawnpoint @a -56 56 -656)
/kill
Player does not spawn at new location (even though command claims spawn is set)
If you reload the world file, then do a spawnpoint command, and die, your spawn is reset. But it only works once per load.
Note, this bug does not occur if you only type /spawnpoint. The bug is specific to typing numerical coordinates.
Is this an intentional change I'm unaware of?
Comments

I still seem to be having this issue in 14w04b.

I think the issue in 14w04b is closer to MC-45971 - the @a is completely messed up on other commands as well like clear.
This issue can be closed. 14w04 solved this.