My experience of using Melodyne inside Sonar has been excellent, sorry to hear you're having such troubles with it.
One difference between our systems is that I have an SSD system drive, and wonder if that might make any difference in Melodyne performance. 
Do you have wi-fi active while you're using Sonar ?
In Sonar Preferences - Audio - Configuration File - what setting do you have for ThreadSchedulingModel ?
(mine is set to 2)
If you watch the Windows Task Manager - Performance Tab while working in Melodyne, do you see large CPU spikes ?
It's possible some windows background service may be interfering.
 
Also, there may be some issues with Komplete audio 6 interface running thru USB3 ports
Some interesting reading from the NI forum site:
http://www.native-instruments.com/forum/threads/komplete-audio-6-clicks-dropouts-cpu-spikes-every-15-seconds.217813/
 
 

I agree with Craig but here are my thoughts as well:
 
• Pitch drift's effect depends on how the note was recorded.  If the pitch obviously varies from the root note—like it drops off, or goes sharp, or starts too low and slopes up—the tool will get it more centered on the note.  You may have to drag, then release the mouse button, and drag again because it makes a very small correction each time.  You may also have to use it and then the pitch modulation tool to fix a note.  Example: you fix a large drop off with the drift tool, but then the whole pitch line is above the desired pitch, so you will have to use a touch of modulation tool and maybe the pitch tool to get things sounding right. Sometimes a pitch slope is good but you have to use your ears and judgment to get the blob just the right amount above of below the set pitch so it sounds right.  You may also want to split the note and only use the drift tool on part of it. 
• Split is funny.  If you don't expand the Melodyne screen to make the blobs larger, you may have trouble splitting.  The split tool is dependent on screen resolution.  In other words, split may not work on a tiny blob until you use the magnifier in Melodyne to make the blobs bigger.  Even then, it may not always split as small a piece as you want.  When you don't think it's working, it may just be because the blob is too small or you are trying to cut off too small a piece.  This frustrates me, too, but it's how it is.
• I transfer the whole vocal at once and then work on it section by section, but that's just me because I am not able to bounce Melodyne very well—something weird about my machine.
• I usually keep ASIO lower—like 64 or 128—until I am ready to do the final mix.
 
You didn't ask this, but if you have any tempo changes, I strongly recommend you transfer the whole vocal into Melodyne all at once so it does not get out of sync.  I have a post somewhere on the Melodyne forum about this because I was having trouble with Melodyne getting out of sync after a tempo change.  If you have a problem with this, I will look for the post and Celemony's answer which was very helpful.
 
Melodyne takes some time to master but it is absolutely awesome once you get it.  You might note that Celemony's videos don't correct things as much as most producers do.  I think that is a public relations thing.

I have an older machine, an i5 760. Melodyne can only process about 1 minute of audio, anything more than that and it seems to run out memory and locks up. I only have a 32 bit install so there is only 3.5GB of memory available in total. I have also had issues with fragmentation and on some projects it's worth my while doing a "save as" in order to keep the project intact, I do this every half hour or so on those projects which are large and have lots of plug ins involved. It's not every project, just the odd one that has certain plug ins that seem to be a common culprit on my machine.
When I use Melodyne I usually make a clone of the vocal track and work on this so I have the original to go back to if needed. I always bounce to clip after every edit, which are usually only single words or small phrases, however I have used Melodyne as a harmony generator and worked on an entire vocal line, phrase by phrase.
I'm not sure but I think I read somewhere that the dialogue box that suggests 1024 samples when you open Melodyne is not necessarily correct and personally I have never had to use anything but 256, which seems to be the sweet spot for my machine. Yours may differ and experimenting with different sizes is definitely worth the effort to find that sweet spot for your computer and interface.
I used to use V-Vocal but I find Melodyne simpler and more user friendly. I know that there are other users here that find V-Vocal easier to use for some effects, however it's not supported anymore so I think it's worthwhile persisting with Melodyne if you can.
There is split note tool in editor that is a one click thing so it's worthwhile finding that to work with. I've found it works simply and quickly.
If you put in some time with Melodyne I think you'll be rewarded with a tool that's fairly simple and you'll get great results. I've watched the tutorial videos but found I had to work with it myself in order to gain a real understanding of the program. Good Luck.

noynekker, I don't seem to have any problems with KA6 and USB3.0. I have had this connected since day 1 this way, and have never had any problems with anything until I started working with melodyne. If I didn't like it so much, I would just quit using it. No internet, wi-fi or anything. I will check the thread scheduling and CPU use.  On the control bar everything looks cool. It doesn't look like I'm using even close to the limits of my system, and yet it behaves exactly like that is the problem. (see rebel007's post above, that describes my situation closely). I am going to try a different approach. I am going to record an acoustic guitar and vocal track only, and fart around with that, and see how far I can push it. I have too many variables in play with this current project (besides, I'm basically done with it, for now at least).
Oh, by the way konradh, I did find all of those tools and took the video "lessons", that's part of the problem, now I'm hooked! I had to fart around with it, and it does some things great, but it's not a magic fix all, you're right. I will report back.  

Thread Schedule Model to 2 did the trick(I was on 1). I had to bump up to 1024 though 'cuz once I started putting it through the paces at 64 samples it started crackling a bit (no dropouts though). I may be able to get by with less, but I decided not to tempt the fates. I loaded the whole vocal track (7:00 min) in and started working on gobs of blobs. complete success!  1024 samples is totally acceptable to me as this is where I start the mixing process, with cleanup. (besides, if I need to continue tracking I can always move it back and bypass the region effect.)Thanks for hanging in there with me guys!

Great news . . . glad you got Melodyne working better on your system. Cakewalk specifically baked X3 that way with ARA to work inside Sonar, but I guess it still may need some tweaks to work on every type of configuration.