Here is the sample code, and I get the exact same results using diffRpt.incomingChangeSets() as I do with the code that loops through the components  (just trying diff things...).  It is strange, it matches the GUI client output exactly until it just stops in the middle...  so, the logic seems valid, the compareTo is not returning the complete set...  This is just quick code, so not robust...

    public List<IChangeSetHandle> findChgSets(IWorkspaceConnection older, IWorkspaceConnection newer, String component) {
        IChangeHistorySyncReport diffRpt;
        try {
            diffRpt = older.compareTo(newer, WorkspaceComparisonFlags.CHANGE_SET_COMPARISON_ONLY, Collections.EMPTY_LIST, null);
            List<IChangeSetHandle> result = new LinkedList<IChangeSetHandle>();
            for (Object obj : newer.getComponents()) {
                IComponentHandle handle = (IComponentHandle)obj;
                result.addAll(diffRpt.incomingChangeSets(handle));
            }
//            result.addAll(diffRpt.incomingChangeSets());
            return result;
        } catch (TeamRepositoryException e) {
            // TODO Auto-generated catch block
            e.printStackTrace();
        }
        return null;
    }

I have determined the mistake I made...  There was a workspace with the same name as the stream I wanted to compare with.  And in my code where I was establishing the IWorkspaceConnection, I sent in the wrong type and said it was a workspace.  So, I was comparing to someone's workspace instead of the stream I wanted...  Obviously this workspace was not complete.

We figured this out by using scm compare.  As a side note, scm compare found both the workspace and the stream and so it said it was ambiguous.  However, I told it on the command line it was a stream.  So, somehow scm compare is seeing both workspaces and streams even when indicated it was a stream...  Not a big deal...