With check-box mode on, I notice that commands executed from the context menu only act on the highlighted selection while the same action from the toolbar will act on those entries that are checked.
Standard I think, although I don't use checkbox mode much myself so my memory of what's possible with it isn't great.
There are commands you can run which transfer the checkboxes to the selection (or vice versa) but you'd have to remember to run them first (or build them in to all your context menu items, which would be a pain).
Hmmm, I was actually cheking it out because the DOPUS zip routine doesn't allow mutiple zip selection for extraction and presents only ADD options in such cases.