Sometimes when I'm programming a Kontakt part that uses keyswitches, I find that the MIDI does not trigger the keys accurately. I remember having an awful time trying to use keyswitches in NI's Session Strings, and now I'm having the same problem with Strummed Acoustic. 
 
I have a palm muted strumming pattern that needs to change to a full strum at the end of every few measures. So I change the keyswitch note for these occasions, and enter the original MIDI note at the start of the next bar to change back to the palm muted pattern. The notes are fully quantized, but unfortunately it's as if Sonar's MIDI is being sent to Kontakt a little out of time because the palm muted note doesn't register in time for the start of the measure - it plays another full strum. 
 
The exact same thing happens with Session Strings - Sonar does not seem to get the keyswitches to Kontakt bang on the beat, and if they're not bang on the beat then the articulation doesn't change correctly. 
 
Is this likely to be a problem with Sonar just not sending MIDI information accurately, or could it be a problem in Kontakt? 

I occasionally get that also, and from the Vienna player as well as Kontakt. I have no idea what's going on there, but it's sure frustrating.

Not at my DAW, but I remember there being a Kontakt setting that basically sets how many beats it will continue when a note is played.  From memory, but I think I remember having to set this pretty short to get KS working properly - well, maybe not proper, but the way I wanted it to.  This was with Strummed Acoustic in non-SONAR DAWs.
 
Same thing with Rise & Hit

Be sure to let me know when you get back to your DAW Bob!
 
I've never been 100% certain that Sonar's MIDI is bang-on, having experienced things like rendered kick drums which were fully quantized start either just before the beat or just after. I remember having a problem with Geist whereby if a MIDI part was looping and there was a kick hit right on the first beat, it wouldn't get played upon reiteration of the loop, and when I printed the audio it looked as if the kick started just before the beat. 
 
 

I don't if this will help, but this is the setting I was referring to ... Latch Mode
 

Oh yeah I looked at that - I have it set to 1/8. I'm not sure if that just affects the chord notes or whether it affects the keyswitches as well. It determines when a chord will stop playing after the notes end - if you have it set to 1/4 for instance, it will wait until the nearest quarter note to stop playing once the chord notes end. 

You can test on Studio One?

sharke
Oh yeah I looked at that - I have it set to 1/8. I'm not sure if that just affects the chord notes or whether it affects the keyswitches as well. It determines when a chord will stop playing after the notes end - if you have it set to 1/4 for instance, it will wait until the nearest quarter note to stop playing once the chord notes end. 

My thinking was that maybe the chord is still playing out a bit after the KS note because of this setting.
 
In a Studio One song, I have latch set to Within 1/4.  The notes extend until 1/8 prior to where the next starts, with the KS note at the same point as the new note/chord.  Works fine in this extremely simple example.

These kinds of problems happen with all key switched instruments, not just Kontakt and not just SONAR.  Though some combinations seem worse than others. 
 
One thing you can do (though it isn't always the best solution) is to load multiple copies of the same instrument into Kontakt and assign them to different MIDI channels.  Then set each one up to a single articulation and use MIDI channels to switch articulations rather than keyswitches.
 
Usually that means separate MIDI tracks in SONAR (one for each MIDI channel/articulation) but you can change the MIDI channel on a note basis in a single track.  I have a CAL script that lets me assign the MIDI channel to selected notes that I use. It is not as nice as say Cubase's expression map stuff but it does work.
 
When loading the same exact instrument into Kontakt multiple times, they share the sample memory pool so it doesn't eat more ram (which it would if you had separate instances of Kontakt).  It doesn't work always though since each separate instrument can't coordinate with the others (reverb/mixing/note cut offs/etc) but it can solve some problems.
 

I haven't had that problem with my Kontakt instruments (not the same as yours).
I generally have my keyswitches programmed between hitting the last note of the old style and the first note of the new.  Not quantized to hit simultaneously with the note you want to switch.
 
I'm not sure if this applies, but hopefully it might help.