I do not have Kontakt... if that happens again, can you somehow see in Kontakt incoming MIDI activity?
Also, check unintended VSTi MIDI outputs (check what is available for any MIDI track input, all VSTs with output enabled will be listed there).
Does any track has MIDI echo enabled (can be if "auto" echo is used)? And if yes, does the problem still there once all echos are disabled?
I mean if there is some "MIDI loop" (unintentional/Sonar MIDI routing bug/etc), that can "activate" all your instances producing heavy load.
Have you already tried stop/start Audio Engine button as a possible quick workaround?