Hey there! :) Hmm, that is strange... I just tried "Context menu item click behaviour" with all possible settings and the context menu seems to respect them.
Could it be that you are changing the left/middle mouse behaviour in the "Popup behaviour" section instead of the one for the "Context menu" section? That could explain it, because those are for the popup icons/engines, and not for the context menu. :)
If it is correct, then we can try something else, if you don't mind. Can you try again with other add-ons disabled, to see if something else might be causing this? Thanks!