This is due to Kontakt's Time Machine pitch shifting engine. For some reason, not known to me, Sonar doesn't reset the time machine's parameters properly, so the samples get sped up or slowed down. I have the same problem with another Kontakt library as well. The vendor suggested that it might be possible to convert the samples bit depth/rate to match whatever your audio interface is set for in Sonar and this could cure the symptoms. I passed on that solution. Instead, I save the the instrument with all of my settings as a new instrument in Kontakt and reload it after reopening a project.
Not a perfect solution, I know...
Regards,
Dan