Have a look at the preferences for the plugin. These are in the Metadata Download preferences. You can also configure what fields can be downloaded from each source. Plus, the Goodreads metadata source plugin has configuration to map the Goodreads genre to calibre tags. Check if something in the configuration might be blocking them.
The metadata download merges metadata from multiple sources. I've never looked at what the rules are, so I don't know how the tags are handled.
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