Hello Doug,
Probably a silly question, but I assume you did actually save the resulting XML file and load it with 'Design tools | Load custom organ' (not 'Organ | Load organ')? You need to use the 'Load custom organ' to make Hauptwerk pick up (recompile) any changes.
If that doesn't solve it, please send us a copy of your CODM organ definition, and we'll see if we can spot the mistake(s):
http://www.hauptwerk.com/forms/support-ticket/