Levels not updating

[Yen]

Two problems regarding updating levels:

First of all, if there are no players in a level it doesn't seem to update properly when you use /updatelevel.

Second, I used an NPC to replace every default bush and rock on my server with an NPC. My NPC went through each overworld level, checked it for bushes, then replaced the level's text (using load/savelines) to replace the bushes and rocks, and updated the level.
Some players, however, are seeing the default bushes beneath the NPCs. Most players (myself included) don't see the tile bushes. However, when a player who DOES see tile bushes picks it up, it takes roughly a full day to respawn.

And while I'm at it, the 'carrying' boolean doesn't seem to be working.