At first I used a modified version of the MyPlot plugin to generate a new plot world and then I switched back to the old MyPlot since the new one has errors. Now when I load the world from a plugin, the world loads perfectly. For the first hour you can join the world but only about 100 blocks far from spawn are loaded. Chunks should be loaded automatically but they don't, and after quitting the server and coming back the game stays stuck on "building terrain". The only way to fix this is to delete the player's data file in the "players" folder or to stop the server manually. Here's my pocketmine.yml: http://pastebin.com/yMkWdQ2Q
The simple reason is because when the plugin was removed, the server lost the generator for the new chunks. When a player joins without the generator, it will attempt to use the default generator, but if that isn't working then I don't know what could be causing your problem.