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@potestus - if you want me to help, please stop abbreviating and using your own terms for things and tell me the specific names of menu items/buttons etc you are clicking on. There is no "sync items" and there is no "mappable items" in this plugin. Do you mean the "Edit Shelf/Tag Mappings" button below the list of shelves in the customize dialog? Please be specific in future.
The error message is a bug I will push a fix for so thanks for reporting that.
As for how the mapping is supposed to work, I have already explained this several times on this thread. I am not going to repeat myself again. Read through the last few pages of this thread and the help file.
In terms of the behaviour you are seeing, I stand by my comments above. Yes a book which has tags of "Short stories, short story" will indeed appear on the "short-stories" shelf with the way you have set these up. However a book which has only the tag "Short stories" will not appear on the shelf when using upload tags as shelves, nor will a book which only has the tag "short story". Specifying multiple Calibre tags for a Goodreads shelf is saying there is a many to one relationship - they all must exist on the book for it to map to that shelf.
The example I keep using is having a shelf called "paranormal-romance" and Calibre tags mapped to it of "Paranormal, Romance". A book with just the "Romance" tag would not go onto that shelf - it is the exact same principle.
So if you want each and every one of the books for that shelf to have that complete same set of duplicated tags in Calibre you have setup currently then yes you could get that approach to "work". However I don't know why you would want to do that. As you have ignored my question asking exactly what it is you are trying to do then I can't suggest anything else.
As for your counts issue, I told you the solution above. If you have clicked the refresh button in the customize dialog, then all of your shelves will appear in the shelves list on that dialog, correct? Then when you click on Edit Shelf/Tag Mappings, you need to click on the green + button to the right to choose which additional shelves that you have added you want to create mappings for. They should then appear in the Goodreads Shelf column.
For when I push that bugfix version I may also just get rid of that second Add (plus) button and have it always list all of your shelves. At one point I had a delete button on there with the theory that you could permanently exclude shelves you had no interest in mapping, but that behaviour all got ripped out and it is probably simpler just to list all shelves for your account.
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