Just a quick follow-up: we have just tested the functionality in our latest officially supported version (Sitefinity 4.2) and everything seems to be working properly. One important thing, that I might have missed mentioning lat time, is that you'll have to make sure that you're not applying the Tag to a state of the document that is not the master state, in which case you won't have it displayed in the backend, since what you see when you click on a documents under Content->Documents and Files is a draft copy created from the master copy of the document. The below sample code will properly assign a tag to your documents, please try it out and let us know if any issues persist.
var taxManager = TaxonomyManager.GetManager();
var taxon = taxManager.GetTaxa<FlatTaxon>().Where(t => t.Name ==
LibrariesManager libManager = LibrariesManager.GetManager();
var myDocument = libManager.GetDocuments().Where(d => d.Title ==
All the best,
the Telerik team
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