doh! How dopey can you get?
Of course the NSMatrix is disabled when there is no selection for the object controller from which it needs a selection. It's actually a fantastic feature that bindings does all this for me! Love it! Now when I actually make a selection, the NSMatrix becomes enabled, and I can selecte and deselect checkboxes to my hearts content.
BUT, it still isn't behaving correctly. Initially NO checkboxes are selected, and there should be some selected. Yet to figure out why this would be.