There are some copy-protection schemes from a few years ago (which some games use) that can cause this, if memory serves. IIRC it can eventually lead to actual hardware damage on some optical drives too. I can't recall ever having problems with direct downloads from Yamaha's website, but that's probably not saying much.

Interesting... All but one of these systems ran the same game at one time (I won't say which, as I think my opinions on it are controversial) and ALL of them had failure of the primary partition (so not the optical drive, but the hard drive) which could be recovered by simply doing an "FDISK /MBR" on it, but the drives would fail shortly after, usually taking another component (RAM, CD-ROM) with them...

Problem there being, the game (A lesser known FPS from around 1997/8) doesn't have copy protection as far as I am aware and the game was played mostly from backup discs, only a Pentium which has never worked properly since this bug appeared, used the original CD.

The optical drives work fine if I place them in another machine and still work fine in other operating systems on the machine exhibiting the problem.

Edit: I wonder if all Win95 boot sectors look the same, perhaps I should image one of the drives and inspect it against one that works, it may give me some insight, I'm just weary of messing up the machine I use for imaging hard drives.

AFAIK, some copies of Sin were infected with CIH. Have you also ran a logged boot (from F8) and see if anything appears out of the ordinary, like copy protection?

I don't have Sin, never played it past the time I loaned it in the 90s. But CIH huh? One of the machines did land up with a corrupted EEPROM. I don't think it is CIH as many of the machines think it is 1994/5/6 so the payload shouldn't go off, but there were others that had similar payloads which might not have the time bomb.

I have located my old Avast 4 installer, it should be good enough to find anything that has gotten onto one of the machines. I will try my K5 as the Seagate in that thing is getting flaky anyway and I have a CF ready for when it breaks, so if I lose everything on the hard drive it doesn't matter much. Amusing thought, I have a copy of a ransomware I wrote named "Tivoli" on there (though I nerfed the payload a little), I wonder if that will be picked up.

Before you say anything, Tivoli had a simple payload, which was to overwrite the partition table and surrounding area with the word "PHIL IS A POOPOO HEAD - DXZEFF" - which is not present on the affected machines, Phil was the name of a complete dickhead where I worked and is the person the software was "written for" back then, the copy on the K5 has been neutered however - it only drops a text file with a rude message. In short, I know it isn't the cause. The only two copies are the one on the K5 and another on a modern machine, it requires manual installation.

My money, then, is on something like CIH showing up.

Progress report, Avast will not run on the affected machines. PC Cillin will not run. Norton will not run.

I think we are indeed dealing with a virus. Also, HDD throughput on the K5 measures EXACTLY 200KB/s, which is weird and, to be honest, shitty, explains why Doom was taking its time loading.

As NT machines are not affected by this, I suppose I could run a VM and mount one of the drives to a Win9X VM running the outdated Avast! - the problem with newer Avast, such as on my Win 7 system, is I know for a fact that it does not detect a lot of older malware.

It wouldn't hurt to try it though. You might also try MBAM while you are at it.
The problem with anti-malware is no program catches everything.

Indeed, MBAM is on the list of things to try as I find it fairly effective.

I'm still stumped as to how it got in personally. I have also inspected the boot sector, it does indeed show small signs of modification though as to the function of these modifications I have no idea.

The corrupted BIOS also showed only minor differences, but those were enough to prevent the system reaching POST. It's settled then, I'll get an XP machine wired in and mount the hard drive as a slave drive on a copy of my Win98 VM... I knew I was right to keep the Core 2 box, it isn't doing anything useful and I don't care if I break it, so that looks to be the likely candidate right now, but I need to find my IDE card as the onboard one does not work and my SATA adaptors suck.

Edit: Better idea, I'll mount a CF card instead as two of the affected machines use those and they are easier to hook up.

This happens all the time on my Win98 box I use for playing around with Aureal.
The only drivers which work for the Nforce3 controller on my machine are the ones WinME loads. However when ME crashes then it does the same thing your screenshots show. I read somewhere that it's a triggered safe/compatibility fifo mode, but I could never get ME to switch back to DMA properly. So I just end up reinstalling the OS. This is with a box that never touches the internet at all, so it's virus free. The only thing that gets loaded are my games off CD.

You should fdisk /mbr and use a live cd with dd to save the first 512 bytes of the disk. Then replicate this issue where it says the MBR has changed, and load up the live cd again and dd the first 512 bytes to another file and compare them to see what changed.