While I do not use Kontakt, I am thinking that the Kontakt 6 overwrote the Kontakt 5 DLLs. Perhaps because the Kontakt 6 CLSIDs are different to the Kontakt 5 CLSIDs , CbB is not finding the CLSIDs for Kontakt 5.
What I would do is reinstall Kontakt 5. Then reinstall Kontakt 6, but this time, see if you can do a custom install so you can specify a particular folder (can be a subfolder of your normal VST folder) for the Kontakt 6 DLLs.
After the reset and scan, I know you will two copies of Kontakt (5 and 6), but at least you will be able to open projects that use Kontakt 5 while being able to select Kontakt 6 for new projects.
It might also be worth dropping a note to Native Instruments to see if they can offer some insight.
My apologies if I am way off. My Kontakt knowledge is very little. Hopefully some who uses Kontakt 5 and 6 successfully will come along and clarify this (or even correct me).