Unclear to me if this is related to some others issues I see in the queue. I have Feeds using Feeds Xpath Parser (7.x-1.0-beta2) creating/updating nodes from a remote site, and correctly creating/associating terms to the nodes. Apparently working beautifully. However, if I visit a term page (even by following the link from the node itself), it claims 'there is currently no content classified with this term'.
It looks like if I edit one of the nodes, rows get created in taxonomy_index for the node's various relationships, and then that one node is associated with the term in a way the term page expects.
Happy to provide more info, or hear any workarounds. Thanks!