Nodes not being associated with taxonomy terms collected in field collection - where are we with this?

Hi, this issue seems absolutely fundamental to the way this module works and yet I can't understand what's happening with it. This issue was closed some months ago but there are others similar to it that are still open, while from what I can work out, this still-open issue would imply that the problem has been solved because it was dependent on this core issue but although the latter was fixed before the latest release of Field Collection and the version of Drupal core that I'm using (7.12), I've still got the problem.

As per this comment in this closed issue, from the point of view of a normal user (i.e. a non-coder like me) when you add a taxonomy term to a node, you want that term to be associated with the node. Why else would you add it otherwise? I have a content type that captures some common elements through normal fields and then allows users to add further details using a field collection, half of which are taxonomy terms, so I've now got nodes displaying links to the selected terms which when clicked return "There is currently no content classified with this term." I've worked out how to display these nodes using views (thanks to this post), but what about when the user just clicks a term as displayed in the node? Is there a taxonomy hack for this, or another module that will help?