It turned out to be a problem in Fiducial List, not in seeding module.
When you place a second fiducial it puts it not in the same Hierarchy node.
Strangely enough the 3rd fiducial is placed under the same hierarchy. Also once you start moving them they all are displayed under the same hierarchy and Fiducial Seeding works ok.
To reproduce: place several fiducials and watch the hierarchy tree display in the annotation module. The second fiducial is not placed under the Hierarchy node.

The new fids are under the correct hierarchy node, Qt is just not updating the tree view in time. As per the tcon today, I'll be adding a new event for it to watch for, triggered on the child nodes from vtkMRMLHierarchyNode::SetParentNodeID (which already triggers vtkMRMLHierarchyNode::ChildNodeAddedEvent and RemovedEvent on the hierarchy nodes), and vtkMRMLHierarchyNode::SetIndexInParent.

Checked in the changes as svn 17991, it seems to work better now, though the seeding didn't update immediately when I had "seed selected" on, I had to go back to the seeding module and then it updated.

Adding a new fiducial while in Seeding module does not create tracts

Fixed event propagation in annotation MRML and Logic to Fiducial Seeding module.
Completed: At revision: 18006