It could be a configuration problem. For example, ChickenChunks.cfg has this option:
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#If set to false, players will have to be logged in for their chunkloaders to work.:Simply add <username>=<true|false>
allowoffline
{
DEFAULT=true
OP=true
}
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Also there is a special configuration rule for Mystcraft dimensions. You mentioned the Nether and Galacticraft, so I don't know if ChickenChunks does something with those...
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#Set to false to disable the automatic reloading of mystcraft dimensions on server restart
reload-dimensions=true
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