Ok, this is a long shot, and may be difficult to answer, but I can't really understand it...
 
I have had some issues with noise in my Studio monitors from my DAW, I realized that most of the sound came from bad electrical cables (not grounded). However I fixed that now. When I play audio from Spotify, soundcloud, Youtube etc, the sound is crystal clear (wasn't before). However when I run a Sonar project i hear some kind of "crackles" and "wining" sound  from time to time. I don't understand this. It is even worse with Native Maschine connected, if I unplug it, some of the noise disappear...
 
As I said, not sure where to begin here, any help very much appreciated.
 
My Specs...
Sonar X3c
Windows 8.1 64 bit
16 GB RAM
SSD 120 GB
ASIO drivers (WDM drivers available, but haven't worked very well)
Sample rate: 44.1
Buffer Size: 128 (also tried 64 and 256)
Bit depth: 24 bit
64-bit double precision engine checked.
 
External hardware.
Motu Ultralite Hybrid MK3 (Firewire/USB)
(I use a Firewire 400 cable with Thunderbolt adapter, with the power supply connected). Only used FW card with TI chipset before, but had even bigger problem then. I tried with USB connection but no change here.
Native Instruments Maschine 1.8.2 (USB)
Native Instruments Kore 2 (latest drivers/software) (USB)
Novation SL MK2 midi keyboard (USB)

I would start by checking your "Input Echo" buttons on ALL tracks (and check for hidden tracks)
 
http://www.cakewalk.com/Documentation/defaultJA.aspx?Doc=SONAR%20X3&Lang=EN&Req=Recording.22.html
 
You could have a "rougue" input active that is feeding noise into your Sonar project (eg an unplugged cable, device etc.)

Hello
 
yeah, seem that this may be a factor, believe I have one or two Input Echos active. Have to check this out later today.
Thanks

However when I run a Sonar project i hear some kind of "crackles" and "wining" sound from time to time. I don't understand this. It is even worse with Native Maschine connected, if I unplug it, some of the noise disappear...

This has nothing to do with your input echo button being enabled. This has Everything to do with your sound card driver and driver settings. Maybe your highest ASIO buffer setting is not high enough for that project. Try 512 and higher. Some projects, especially with allot of plugins, need more resources. 
 
As your project grows, you may need to raise your ASIo buffers from 64 to 256 and from 256 to 512. It all depends on many mitigating factors specific to that project at hand.
 
CJ

Hey CJay
The annoying sound is there even with few Plugins. The MOTU drivers are the latest, and the electrical "zumming" or what I should call it is present even if I don't hit the play button. I have tried both 256 and 512 ASIO Buffer and even WDM drivers.
 
As Boydie suggests the link from CW above seem worth trying out. However, not sure if I done this correctly
When deselecting the blue icons it works for a while, however it is highlighted again if going from another channel back the one with Input Echo selected.
 
" />
 
Can there be another feedback issue like this below?
In the documentation in the link above it states...
Note: This procedure does not eliminate feedback from your system, only the echo. If you experience feedback, you have a feedback loop somewhere in your mixer setup.
 
I am not sure how to check this?

I'm experiencing the same thing.
 
I have input noise on one or more channels on *every* project I open in X3C. 
Those same projects have NO noise in X2. I've tried 3 different audio interfaces and the behavior is the same.
X2 - no input noise at all.
X3C - noise on multiple channels even with NO input monitoring and channel input set  to "None".
Very strange and frustrating. 

Disable 64 bit precision engine. See what happens.
BTW always a good idea to update your footer with your specs (see my footer) then we know what your system is. Cheers.