Is it possible you are seeing the kontakt loading pane?

As to the input going to multiple Kontakt channels, two possibilities: Kontakt is set to "omni" in the midi input field, or you have sonar's "echo input" active and the echo goes somewhere other than the original midi channel.    As to some of the things in this long and good thread, I'm now using many instances of Kontakt 5 and hundreds of loaded instruments, many gigabytes of memory.   The only thing I take care about is to consistently use the same Output channel format in every instance.   In my case, I use the "16-outs" version, with four stereo outputs, (and the aux outputs) and group different instruments and banks into one of the four; each gets a name, as Bob initially said, and that's not a problem, but following the K5 manual I don't mix instances with 2 outs with instances with 8 outs or anything like that.
 

(R.E. Screenshot) That looks very possibly it, although many of Kontakt's preference screens have the same GUI format. I might try Bob's suggestion or just run a screen capture utility. Speaking of the screenshot - I noticed the LoopMIDI icon - another great little utility!  Thanks to all in this thread, lots of great, helpful info.
 
I also seem to have had issues with Sonar (from 8.5 to current) that cropped up mainly during projects using Kontakt (4 & 5), but other than the oddity I mention regarding the window "ghosting" lately when I make track templates, I have found no easily reproducible pattern. I do seem to find, that careful use of the multiple output .dlls, -rather than the seeming default that loads 64 outputs (do heed the tips here on re-naming the instances in plug in manager - very well advised) cuts down on the times I will have crashes or inconsistency. Seems like it would save system resources at the very least, if one is not going to use that many outputs in the first place.
 
On my end, I seem to experience odd crashes or inconsistency the longer I play around with adjusting parameters while playback is running (tone adjustments, drum mixes, whatnot), and the odd crash on opening a project that has a fair-sized Kontakt sample library to load up (I see the loading window briefly..) after running & closing any number of other seemingly unrelated projects beforehand.. Hence my wariness of the "ghost" window I see when making a track template...  Maybe it's unrelated, but I am exploring all angles.
 
Other than that though, the majority of the time Kontakt & Sonar work great for me, and organizing (and cleaning up) the outputs section, customizing the multi-out defaults and such, as mentioned here, has really made the difference in workflow, and again, I think maybe cleared some problems up as well. So again, excellent thread folks!  -Jn-

Under some circumstances all your efforts to create friendly names for your plugins will all come to nought because a plugin reset or scan can return the plugin to its default name. You can however change the default name that Sonar uses by creating and using a variable in the Sonar Cakewalk.ini file as follows. It's a one time thing.

VSTPluginNameFormat=2 this allows me to see the full dll name. It obviates the need for friendly names.

Can be 0-3. As defined below,
0 = VST Name
1 = DLL Name
2 = VST Name (DLL Name)
3 = DLL Name (VST Name)

See page 1578 in the reference manual for more details.

williamcopper
As to the input going to multiple Kontakt channels, two possibilities: Kontakt is set to "omni" in the midi input field, or you have sonar's "echo input" active and the echo goes somewhere other than the original midi channel.    As to some of the things in this long and good thread, I'm now using many instances of Kontakt 5 and hundreds of loaded instruments, many gigabytes of memory.   The only thing I take care about is to consistently use the same Output channel format in every instance.   In my case, I use the "16-outs" version, with four stereo outputs, (and the aux outputs) and group different instruments and banks into one of the four; each gets a name, as Bob initially said, and that's not a problem, but following the K5 manual I don't mix instances with 2 outs with instances with 8 outs or anything like that.
 

Got it pretty much figured - although I don't use the aux as I don't know how to. But yes, I'll have a look at that echo input, which is where I may be getting some spill. Today I experimented with initially one instrument and set it up and did the 'Presets / Batch Configuration, and click on that arrow to expand that, then hover your mouse over the 'Batch Functions', and when the options open to the right, click on 'Clear output section and create one individual channel for each loaded instrument' and then added another and did the same thing. All went well and it's good to be able to able to do this, so now I can load a number of instruments instead of several instance of Kontact. Very effective. Thanks to Bob.

In case this is useful to somebody I learned this today...
 
Crackling and volume issues keep resetting within Sonar - How to Resolve...
 
1) Update Kontakt in service center.

2) Check this post:
http://forum.cakewalk.com/FindPost/1106242
 
3) Remove or disable the convolution reverb for each instrument if it exists, this is crackle central!!!:
Wrench button > Insert Effects -> Conv.
 
If you really need to use convolution reverb use it as an aux.

I'm glad I stumbled across this thread, seeing as I pick up Komplete 10 tonight!!

Mudgel, I did not know about the vst name format setting. This is great! Thanks.

Wish I knew about the VSTPluginNameFormat setting  a long time ago. I just added it to the ini file. So simple. So useful. Thanks again Mudgel.

Piggybacking this useful info:
http://forum.cakewalk.com/m/tm.aspx?m=3279578