Are these Mavericks tags? Check this by selecting a document in Finder and look at File > Get Info. It’s possible that some process is adding Mavericks tags to documents, which will show up in DEVONthink as DEVONthink tags when you import the document.
If I remove the ghost(?) tags from the PDF files in DEVONthink (Inspector, press ‘delete’/‘backspace’ for the tags in the tag window), they reappear again.
But if I look in the total Tags list, and click the ghost tag (there are some legitimate files that I’ve tagged with the ghost tag, but there have been other files where the tag applies itself automatically and refuses to be deleted), the files with the ghost tags are not there.
So, you see the tags in Show Info. You see the tags in the Tags bar. You don’t see the documents in the Tags group for that tag. What color are the tags? Blue or gray? Do you see the tags in View as Tags? Do you see the tags when you export the document (in Finder Get Info)? If you select one of these PDFs with zombie tags and look in Show Info – are there any duplicates or replicants listed at the bottom of the Show Info panel?
How about making a screen shot of the Show Info panel and Tag bar for one of these PDFs? It’s getting difficult to visualize exactly what’s happening here.
But I’ve found the source of the disease and fixed the problem.
Turns out that the entire folder had the two tags inside (not sure why, as I don’t tend to tag folders. Must have been an accident late at night). I’ve removed the two offending ghost(?) tags from the folder/‘grouped items’ and now everything’s sorted.
Is there any way where I can filter the files that are have no tags?