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By MrPolarBearJ
#125174 Make sure your worlds have this in them:
[*]1. locate the worlds folder in the server folder
[*]2.Copy the "forcedchunks.dat" file and paste it in the folder of the world you wish to have pixelmon in

Source: viewtopic.php?f=85&t=12696

If that doesn't work, you could always just do a single player world and copy the world file from the minecraft saves folder, into your server file, and import it. That's what I do, especially since I try to make my own custom maps. But I also use world paint after creating the world just so I know the files for pokemon to spawn/etc are there. Then I basically build the world to my liking then use MCedit for minor details. :) A lot of work, but gets the job done. :)
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