It turns out that the filecheck plugin couldn't find the file, because it was merely using the $pagesources hash, rather than finding the absolute path of the file in question.
+> I don't understand why the file was not in `%pagesources`. Do you?
+> --[[Joey]]
+
The following patch fixes the problem:
diff --git a/IkiWiki/Plugin/filecheck.pm b/IkiWiki/Plugin/filecheck.pm