I examined the ecf file for this project and found that the base folder for the library is: <cluster name="opencv" location="C:\Documents and Settings\Chris Saunders\My Documents\Eiffel Projects\library\OpenCV\" recursive="true">

Later when I added the new subcluster this was added: <cluster name="support" location="c:\documents and settings\chris saunders\my documents\eiffel projects\library\opencv\support\"/>

Apparently the recursive was not taken into account by the Cluster tool.