Hmm, I just updated my Kontakt 5 to the latest (v5.8.1 , R43) a couple days ago using Native Access, then did a manual VST scan. The updated DLL files were just there in my designated VST folder (No further action required).
After reading your post, I loaded Kontakt 5 into a project and the latest VST2 version shows up fine.
Check the dates of the kontakt DLL files in your VST folder, and confirm they were recently updated. Also, after the manual scan, make sure there were no errors.