Tone board is connected to JDS Labs Atom AMP. I am using that combo to drive Beyerdynamic DT990 Pro 250 ohm. How can I be sure that it is ground loop? I don't hear anything while playing or idle, only when connecting new things to my PC..
Weird. A lone Y capacitor (single-digit nF range) in the Atom's power supply aside, there is very little potential for ground loops. You do not happen to live in a very dry climate by any chance? If so, does just touching the PC case do something similar?
OK, sanity check time - what is master volume on the PC set to? If below 50-80% (-10..-3 dB), increase to this range, and reduce volume (and if needed, gain) on the Atom correspondingly..
With that out of the way, I would want to test whether it is an analog problem or in fact an interruption of the audio data stream.
Would you mind generating a low-frequency sine (like 50 Hz or something - the tone generator function in Audacity is perfectly fine), playing that back and then plugging/unplugging your keyboard or mouse?
If it is a purely analog problem, the crackling would be equally loud as without the test tone.
If it is a problem on the digital side, playback of the test tone may turn the crackles into major cracking noises.
Also, try a USB output in a different location to see whether the issue occurs everywhere. Ports at the back should generally be the safest, and USB3-capable ones may be more robust in terms of power delivery than purely USB2 ones. Long, thin cables to a front port may cause momentary dropouts as things are plugged in.
To rule out that momentary power loss is causing the issue, you can try running the DAC via a
powered USB hub.
Download and run the tool
LatencyMon to make sure DPC latency is within reasonable limits.
If nothing else helps, I would try another DAC... possibly via Toslink as suggested, assuming your board has an optical output. (Note: D10s has an optical output only, E30 has an input.)
Speaking of which, have you tried the onboard audio yet? A higher-end board may be using a Realtek ALC1220, which actually is pretty good if the implementation isn't screwed up by the board manufacturer. Achievable dynamic range is as good as any low/midrange DAC, just distortion performance doesn't make it much beyond -90 dB, but that's still inaudible.