It seems that Kontakt 3.5 or even 4 may need an update to be compatible with Logic 9.1 in 64 bit mode.
In standalone mode Kontakt is 64bit... but in Logic it still is 32bit.
Plugin developers are now just beginning to announce new 64 bit versions for the Mac. Spectrasonics and East West are among the early birds.
There are other users calling for a 64bit version:
Hope that helps