Hmms I was told that you have a bukkit plugin that deloads any chunks that don't have players near them. And from what I've seen there has to be something like that in place. For example, when I was making my rail connection I left some cobble on the ground, then went back to the spawn. In single player, that cobble would disappear after 5 minutes. However half an hour later when I came back it was still there, suggesting it had been saved in that force unloaded chunk before it could disappear.
Also I went and checked out trashmans place in the middle of the day, and there was mobs everywhere, burning. Those mobs had to have been saved in the force unloaded chunks, else they would have died as soon as the sun came up, not in the middle of the day.
I've been playing single player for several months now and havn't seen this behaviour before.
EDIT: Read the wiki, and it says in SMP the amount of chunks that load around the player is configurable.
Now a mob will instantly despawn if the player gets over 128 blocks from it. So, if we want mobs to despawn, you would need to set the chunk radius such that the amount of blocks around the player is greater than 128 in every direction. 128/16 = 8 chunks, so the radius needs to be at least that. The default radius is 10 chunks, so that works nicely.
However, I'm guessing warping would interfere with this, and may be the cause of our problem, since when you warp the chunks that you were in would instantly go inactive, possibly before the mobs in it have a chance to despawn.
Not really sure how you could fix that besides disabling warping. But we do have a nice rail system in place so it wouldn't be that big a loss.