I'm a dev for PracticalPlants.org, a semantic wiki of plant use information. We've had long running mysterious problems with Cite which have been difficult to pin down, but since upgrading to MW 1.20.3 and Cite 1.20, the problem has become much worse.
All our references on plant articles are at least 2 templates deep - the first template is a template used with semantic forms, the second is the Ref template we use.
The result is that Cite outputs the following Cite error for every reference:
Cite error: <ref> tag with name "PFAFimport-1" defined in <references> is not used in prior text.
The ref tag name is most certainly used in the prior text in all cases. The <references> tag is placed after all <ref> (actually {{#tag:ref}}) calls.
If I place a <ref name="PFAFimport-1"/> or use our ref template {{Ref | PFAFimport-1}} directly in the wikitext after the semantic forms template then Cite lists it, so it seems like it's something to do with it being in a second level template. Again, the ref tag with that name is certainly being output, and indeed it's rendered inline as a reference, it just fails to list it in the <references> section.
Has anyone experienced anything similar? Anyone have any ideas?