I’m experiencing the same problems too and it has occurred over 10 times since I bought the Strix X399-E last October.
The VRM/COV fan would spin up to max RPM and stays that way even after restarting the system. Only a cold boot would return the COV fan back to normal. The Zenith X399 boards also have issues with the COV fan.
Today, my system shut off suddenly while I was watching a 720p movie. Besides that, there weren’t any other apps running so the system was pretty much idle. I doubt the cause for this was due to a power surge as we rarely get that. I suspected it was the board’s fan controllers failing again so I immediately I turned the system back on to check the temps. I found the CPU was around 70°C and was decreasing quite rapidly back down to my idle temp, 32°C. My usual load temps are around 58°C, and watching a low res movie wouldn’t stress out a 1950X with an Enermax LiqTech 360 to over 70°C. So it only makes sense that the fans and pump had stopped, the CPU temps rose too high and in order to protect the system, it shut everything off immediately. While I agree with Gupsterg and have found that using multiple apps that monitor your hardware increases the likelihood of PWM issues—and I’ve stuck to using just HWiNFO ever since—however in this case I wasn’t using any of those apps.
Also, it doesn’t take a long system up time for the motherboard’s fan controllers to malfunction either as I’ve found in a Realbench stress test I did. After cold booting the system and launching Realbench, the fans failed to ramp up as it should when I began the test and stayed at a low RPM. The CPU temps rose to 78°C before I aborted it.
In another instance, the CPU and case fans malfunctioned during 3D rendering and it kept spinning at max RPM 10 minutes after I’ve closed the app and left the system idle. Going into sleep mode temporarily and waking the system would usually return fans to normal.
I use Aura’s temperature preset and even that gets bugged, and stays red when it shouldn’t be.
So from my experience the fans can malfunction at any moment, it can stop completely or freeze at a certain RPM, under heavy stress or when idle. Aside from the aforementioned bugs, my system is stable. I currently run my Threadripper 1950X at stock, 3600MHz memory at 2666MHz, though I have stress tested and passed reliably at 4.0GHz/3200MHz. It has passed 14 hours of Memtest (DOS), 20 hours of HCI Memtest (Windows), hours of Realbench, I’ve done way too many stress tests, thanks to the confusing fan malfunctioning bug, to confirm that my RAM and everything is 100% stable, and that the problem points towards the BIOS (0402). It’s been over 4 months since we got an official BIOS update. Until they’ve fixed these major problems, I would not be recommending this board to anyone.