Based on your sample doc, make changes to each of the Tag properties on the checkboxes so the Tag matches the text on the checkbox. This means each checkbox tag could be Yes, No or NA. Then try this text which will also ensure that you can only check one box at a time.
Code:
Private Sub Document_ContentControlOnExit(ByVal CCtrl As ContentControl, Cancel As Boolean)
Dim lngColour As Long, i As Long, aCC As ContentControl
If CCtrl.Type = wdContentControlCheckBox Then
If CCtrl.Checked Then
For Each aCC In CCtrl.Range.Cells(1).Range.ContentControls
If aCC.Tag <> CCtrl.Tag Then aCC.Checked = False
Next aCC
Select Case CCtrl.Tag
Case "Yes"
lngColour = wdGreen
Case "No"
lngColour = wdRed
Case Else
lngColour = wdAuto
End Select
CCtrl.Range.Font.ColorIndex = lngColour
Set aCC = CCtrl.Range.Rows(1).Range.ContentControls(1)
aCC.LockContents = False
aCC.Range.Font.ColorIndex = lngColour
aCC.LockContents = True
End If
End If
End Sub