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Sorry for your trouble! Can you give me step-by-step instructions of what you're doing and what is happening after each step? For example, from plugging your CueCat/s in to using certain pages on LibraryThing (links to each page you navigate to and where your cursor is on the page for each action), to actually scanning the barcodes?
A few helpful things to do/try, if you can:
1. Can you send me clear photo/s of a couple of your barcodes to make sure the issue is not the barcodes?
2. Have you tried scanning-to-add a couple of books by their ISBN barcodes, for troubleshooting?
3. Have you tried plugging into a different USB port?
As for editing "Subjects", this field is not editable I'm afraid. It sounds like that data is getting pulled in from other editions at the work level for The Christmas Carol (which is a pretty large work).