I was sent this message:

"We had discussed this in the past and decided that subcluster is an abstract representation of classes, but in practice it is as if you had 2 clusters. Sowhen you include twice the same cluster, you end up with the same classincluded twice, thus the error."

I still believe that this represents a bug in the tool (the "Clusters" tool).  If I add a cluster then the tool should be aware that recursive has been set for the parent cluster and do the "right" thing in the ecf file.  Note that the tool is clearly doing something that is clearly wrong and should not require that one remembers that recursive has been set and therefore the tool can't cope.