I’m using straight 0.9.6 rev 2767, MySQL 5.0.22, PHP 5.2.5. I ran the supposed query that the manager uses (line 98 of /manager/frames/nodes.php) to display the docs in the tree:
SELECT DISTINCT sc.id, pagetitle, parent, isfolder, published, deleted,
TYPE , menuindex, hidemenu, alias, contentType, privateweb, privatemgr, 1 AS has_access
FROM modx_site_content AS sc
LEFT JOIN modx_document_groups dg ON dg.document = sc.id
WHERE (
parent =0
)
GROUP BY sc.id
ORDER BY menuindex
And it correctly displayed the docs in the right order, so my guess is that the "order by" field is either not being used or is always being passed as "id". I don’t have logging turned on at the Prod server, but I may do that soon.