FIGURED OUT THE PROBLEM WITH THE UN-RESPONSIVE CHECKBOXES IN MY UITABLES!!!!
It turned out to be an insidious problem that Mathworks should really "fix".
In stepping through code, the checkboxes worked fine up until I set data. It turns out that when calling a "set" to assign data, I was trying to assign checkbox a value of 1 or 0. That isn't good enough, as their class is "double". You have to assign the checkbox fields "logical(1)" or "logical(0)". The "logical" function converts "1" and "0" to class "logical". That is completely stupid. No warning was given when I made that assignment.... it just locks up the checkboxes.
From my previous example, setting my data (for my 3x3 table of checkboxes) should happen like this:
Data = [ 1 1 1; 1 1 1; 1 1 1; ];
DataLogical = logical(Data);
set(handles.uitable1, 'Data', DataLogical );
Another problem I found (with OR without GUIDE) is that IF you position your Table window in a way that interferes with other objects, the check boxes are unresponsive. Nice. Re-position them to have plenty of room around them and the checkboxes (AND combo boxes) behave normally again.
In general, many MATLAB GUI components (independent of GUIDE) behave badly or don't even display at all if you give them invalid values.