@Noughty - you can't do that. You must specify only one column in Calibre to represent your Goodreads shelves - either a custom column, or a tags column. Once you have made this choice, you can then sync the two together by either modifying the value in that column and choosing upload, or modifying your shelves on Goodreads and choosing download.
BTW if you are still seeing those messages you reported earlier from debug mode of "get_categories: xxx not in list" etc I will still need you to do what I requested previously of uploading your metadata.db to somewhere I can take a look. I'm glad all your other search/tag download issues are resolved.