So the skylands has places where you everything is dark and you seem not to be able to place blocks. Also, the minimap is messed up there. You try to place blocks but cannot see anything happening. However when you leave the area (unload the chunk) and come back, the blocks that you tried to place but could not see, are actually there. Also, now the chunk properly displays in the minimap. The whole chunk that was first compelety invisible, is suddenly there.

It seems to me that only completely empty chunks are affected, those where there is not one single block. I am not sure if that is a bug where bukkit does not load chunks w/o contents or if there is a different issue. Clearly the map files are OK. Dynmap also renders the map w/o the issue the minimap has.

So I am not sure what has to be done to fix this issue. I posted this now at first to the author of the skylands plugin. I will see if we need to escalate this to the bukkit team.

This has the following consequences: If you have an empty chunk in the skylands where you cannot place a block, place one, go to spawn, come back and it should be fine provided that no-one else is in the area. This is a good workaround for now. Latest after the server restart, the empty area will be fine – if you at least attempted to place a block there.