Drives randomly dropping out (once per boot cycle) I/O error

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Ok, this one is a bit of a puzzler.

Background

I have 4 hard drives, one boot (SSD), 2 western digital reds, and an old seagate.

I boot my computer up, play around some, and then, suddenly, all of my non-boot drives give i/o errors. I can still access my C (boot) drive, but using explorer to try and access any other drive returns an i/o error, note: the drives all appear in explorer and report their storage capaciaty.

I run diskmgmt.msc to see what the problem is, they all work again and the problem is as if it never happened. It does not occour again for the remainder of the computer's time on, and only happens once the machine boots.

It started to crop up a few months ago.

Solutions Attempted

Scanned using avast, malware bytes and spybot search and destroy (each one done in safemode); 99.99% certain it's not a virus

Run checkdisk on all drives, no errors reported, no bad segments found.

Booted on a linux pen drive and ran with no issues on there.

Current Hypothesis

During the fall update, my start menu was entirely borked, I am suspecting that it may be a borked setting somewhere (the linux test has ruled out bad hardware for me). It is also strange that it only hits my storage/backup drives and not my main boot drive. Anyone have any ideas before I give in and create a new profile?

 

[JaredDM]

Just a guess here, but it could be that one of your non-boot drives has some slow reading sectors in the MFT. At some point the OS tries to read part of the MFT and it stalls and locks the SATA bus out to the other drives while it's in a busy state. Until it eventually gets past that point or gets interrupted.

Your OS drive perhaps is on a different SATA bus, which is why it's not affected.

As a test, I'd try keeping them offline one at a time until you find which one is causing the problem.

If it's not that, then it's probably an odd hardware issue perhaps relating to your motherboard. I highly doubt it's software related at all, but you never know.