I didn't even think about the CPU, but I would definitely not rule that out. I have no experience at all with integrated graphics, never had a CPU with that. I don't know if it's possible that the CPU is doing the desktop rendering, which might explain your issues.
I installed the new CPU (with no integrated GPU) and the audio drops/artifacts still exist. For now I'm just setting screen to 1920x1080 and using analog stereo. I've yet to contact Sony about the amp because I think the limited warranty period has passed. I'm not really sure how to resolve this? Kinda sucks because I hoped a dedicated PC with dedicated video card would have dominance over a laptop or shuttle PC. Games run fine on it! ha ha! I wonder if settings the system to real-time kernel would make a difference? Maybe the audio is a latency issue? https://ubuntu.com/blog/real-time-ubuntu-is-now-generally-available
