Fixed in the next build. Or rather, fixed the problem described below:
This occurs whenever a page is edited in an automated context, where the change requires a new revision to be created for the page but a revision was not expected. I don't know of a specific situation where this happens but if it does, in this case, a template forgets that a page that was updated in this way is using it. The bug first appeared in 4.0.9.
A future upgrade script will attempt to regenerate the forgotten entries.