Unresponsive during disk I/O on first boot

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RobWithTheBigPC

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Brand new system, so hard to pinpoint cause. Symptoms: on first boot, the mouse will seem unresponsive. Freezes up, moves in little jumps, low sensitivity. Keyboard, similarly: types keys buffer for a second or so, then all appear at once.

Then the system will work smoothly for a few seconds. Then go back to being unresponsive. The unresponsive-ness seems to coincide with disk activity. If I see the disk light flash, or I open a file or start a program, that's when it will be unresponsive for a few seconds.

If I reboot, everything is now fine. So it seems like something to do with a difference between a cold start and a warm start. That makes me think of firmware/BIOS/drivers.

System:
X870E Carbon
9800X3D
MSI Ventus 4080 Super
NZXT 1500W PSU
2x24GB memory at EXPO 6000MT/s
3xWD Black SN850X 4TB SSDs (in slots 1, 3 and 4 to avoid lane sharing)
Windows 11 24H2
Most BIOS settings otherwise default apart from turning on EXPO and disabling iGPU.
AMD_Chipset_6.10.22.027 drivers
BIOS 7E49v1A21 2024-12-20
 
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Minor update: the advice so far is to clear the CMOS (I guess to erase any weird settings I might have done) and to update to the latest chipset drivers (which I have already done).
 
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RobWithTheBigPC said:
3xWD Black SN850X 4TB SSDs (in slots 1, 3 and 4 to avoid lane sharing)
Click to expand...
WD 800 series drives are known to be a problem along with the Samsug 900 series please check WD for firmware updates for the M.2 drives
 
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citay said:
Well, Clear CMOS never hurts to try. Worst thing that can happen is to lose a bit of time on it.
Click to expand...
Well, I just did that by holding down the reset CMOS button on the back panel for 15 seconds.

Now I can't get past 97 on the diagnostic LED. That's "Console Output devices connect". Possibly GPU related. The GPU has been fine until now. So it's some comparability thing.

I've tried rebooting, resetting, and completely cutting power. I'll keep at it. Suggestions welcome.

Edit to add: GPU fans are spinning, monitor is lit up and displaying a small cursor top left.
 
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Ok I cleared the CMOS again and now it's booting.

This time I turned off power at the PSU and held the button for almost a minute. Not sure which of these rituals fixed the problem...

Now I'll put my settings back and see if the original problem (lagging mouse / slow CPU on disk I/O) comes back.
 
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Each new bios version fixes one problem and creates two. Now I have frequent freezes, you have to unplug the PC, but when you turn it back on you lose the wifi. Then I need to clear CMOS and set everything up again to get the wifi back.
 
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I like to hear more it's hard, or it is annoying than creating more issues, before you hijack someone topic.

RobWithTheBigPC said:
GPU fans are spinning, monitor is lit up and displaying a small cursor top left.
Click to expand...

I understand you don't have problems without GPU. Is it an old GPU? I heard people saying some needed to flash to a new firmware to make it work in a new system. But careful you get it, if needed, from the original supply website.

Edit: Ok I see you have MSI Ventus 4080 Super. No need to flash that to make it work.
 
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Return the defective board to the retailer and get a different one.
Even the 600 series AM5 MSI boards are full of issues - some are not getting fixed for more than a year now.
 
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citay said:
Are MSI suggesting anything to try?
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Since I reset the CMOS and that did not help, MSI have suggested updating to the latest BIOS (as of 2025-01-21 which I had not yet seen) and also turning off EXPO. I'll give both a try next. There are also new chipset drivers 7.01.08.129 as of 2025-01-22 so I will try those.
MadSky said:
Return the defective board to the retailer and get a different one.
Even the 600 series AM5 MSI boards are full of issues - some are not getting fixed for more than a year now.
Click to expand...
It is a worry. I retain some optimism for now just because it is early days and there are still frequent updates. Let's see how it goes...
 
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Well that was a bit too exciting...

I flashed BIOS 1A23 using M-Flash as suggested by MSI support. The machine no longer would boot. It would reach b4 on the diagnostic LED and the reboot, repeatedly. I tried resetting the CMOS again but that did not change the behaviour. So I flashed back to 1A21 using the Flash BIOS button on the motherboard...the first time I have ever had to do that.

Now I am running 1A21 with completely default settings (including no EXPO) thanks to the CMOS reset and I have already reproduced the problem.

Perhaps I will try 1A23 again and/or update the chipset drivers when I am feeling a little more brave again.
 
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I don't want to speak too soon but since I installed chipset drivers 7.01.08.129 I have not seen the problem. I also haven't used my PC quite so much so I'll leave it a few more days before calling this solved.
 
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An update: I did speak too soon. The problem came back. Maybe not quite as often. But I think I have finally fixed it: I have not seen the problem in a dozen boots since I made the following change:

In BIOS, in PCI settings, change all the PCI speeds from AUTO to the speed you need. Since upgrading to a 5090 it became more apparent that the PCI speed was stuck on x1 when the problem was happening. So I set the PCI speed for the GPU from AUTO to x5, and since all my SSDs are x4, I set the PCI speed for the M.2 slots to x4. Since then, every boot has been perfect and the problem has not manifested (and it's obvious immediately upon logging in when it is happening because the mouse keeps sticking, making it hard to get to the start menu to reboot).
 
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I don't want you to encourage you, but I think your problem is not solved. PCI speed is set by an algorithm, if it doesn't set automatically, something is wrong. You have it on multiple devices, so this brings me to the software/setting. On boot, the PC has a lot to do (even with triggered task), and when there is not enough power coming from the PSU to the CPU the mouse could stick. Could too explain why that PCI speed is preferred by the software. You have a 1500W PSU, so don't think that would be the issue. May I ask before we continue... did you undervoltage the CPU? It's not a necessarily to have this issue, but it helps to understand what could be done. And if so how did you do, and how far did you get?
 
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