I've got an extremely large (~15,000 topic) publication which is itself made up for 5 smaller but still sizable sub-publications. The content is the result of and conversion and import from a wiki-style product called "wikidot" and is still very much being cleaned up by its authors, so that could be a part of what's in play here.

However, when I publish the main publication, or even one of the subpublications, I see a strange behavior where content is rearranged and grouped under topicheads. This behavior is addressed by removing the topicheads and replacing them with topicrefs and stub topics, but overall this is not a good solution. The content seems to be clustered under the navtitle of the last topichead in the current submap. For example, here's how it looks in Publication Manager:

And here's how it looks in the output:

Interestingly, this problem only afflicts the output in the Webhelp output format; the Eclipse help output format behaves as expected.

Has anyone else seen behavior like this?