Please create a support ticket at
http://www.automaticduck.com/support/contact and attach your zipped logs folder to the form.
It sounds to me like the MXF media isn't actually the media the AAF file is expecting to find.
The logs will tell me which files the plug-in was looking for and couldn't find then I can communicate with you about where those files are located.
-- Wes Plate
Automatic Duck