I also have this problem. Yet it only occurs IF i log off close to the thaumcraft dungeon with an evil node inside it. This dungeon is fairly close to my starting area, and after a night sleep, I can log in, and i will immediately see what the OP has shown us. If i then unload the chunk (by going far enough away) and come back they are all gone. The chunk the node is in is not covered by any chunk loaders.
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