It looks as if you have Chunk errors. Chunk errors can be caused by plugins malfunctioning, or not setup correctly. The jar on your server not being stable, or someone spawning in too many entities.

You can also use Program MCedit.
http://www.mcedit.net/

Here is a great tutorial on fixing chunk errors with MCEdit.
http://www.youtube.com/watch?v=bRfxdIQfUPQ