Strange Block updated (not correct block updates)

When creating an custom world with my plugin some block updated won't work properly anymore.

Dirt won't update properly to grass
Crops won't update properly to their next stage

The updated block will spawn some blocks above the original block. In some cases the 3th stage will spawn above the 2nd stage.

Even blocks placed by hand will do this.

This won't happen in the Minecraft overworld and in a custom world that is created with another plugin.

The plugin that created this terrain does nothing but creating a chunk

This chunk in the photo is generated with regenerating the chunk (the method deprecated), I don't know if this is the problem...

I hope this will be fixed, or somebody can help me this this

 

Maybe you can try opening the world in mcEdit or something like that and then reexporting it. I am guessing that the world file is corrupted. Maybe even just restarting the server can help.
I hope i could help!

- xXraxFraeyXx