I had the same problem at one time. It resulted in multiple versions of Kontakt co-residing on disk, which took me awhile to notice. It wasn't until I updated Kontakt to fix a specific bug, and the bug persisted after the update, that I figured out what was going on.
 
The problem was self-inflicted, caused by me attempting to keep my plugins organized. The solution: don't fight the installer. Let NI install files in whatever default location it wants. I deleted all existing copies of Kontakt*.dll, re-installed, located the newly-installed DLLs and added that location (c:\program files\native instruments\vstplugins 64 bit) to SONAR's VST search paths. It annoys me every time I see that path in there, but it solved many problems.