It happens sometimes that certain notes aren't as loud as others, but it ain't supposed to work that way. Library developers carefully level-match samples to avoid that, so it sounds like somebody goofed when the library was made. You might want to let them know about it.
In the meantime, you could try to mitigate it with volume automation. That'll work if the part's not overly busy. I'd do it with MIDI CC7 automation, so that once compensated you won't have to worry about it again when it comes time to automate the volume on the audio track.
Of course, if you're handy with Kontakt you could fix the problem yourself. But that entails per-sample volume adjustment, so I wouldn't recommend it unless you're already comfortable fiddling with Kontakt sample mapping. Even if you're not, you can safely experiment with it - just copy the .nki and work on the copy rather than the original.