Might be running chkdsk in the background hence why it's taking 2 minutes, you could of course just disable it running on startup. Make sure the SMART statuses of the SSD are all OK and reading within limits to ensure there is not an actual issue with the drive.

Don't forget about the write amplification issue on XP, especially when using NTFS on an SSD (Better using FAT32). Remember to disable the swap file, background defrag and windows prefetch. You could also turn off system restore and error reporting. Bit extreme but if you really wanted to speed this up and eliminate unnecessary writes then disable last file access time updates.

CHKDSK does not run in the background.

The cause has been found: IDE Primary Slave, in my case the DVD drive.

I arrived to this conclusion by starting up Linux Livecd in verbose mode, then checking kernel logs. The device ata1.01, which identified as my DVD drive, kept throwing this:

ata1.01: exception Emask 0x0 SAct 0x0 SErr 0x0 action 0x6 frozen
scsi 0:0:1:0: CDB: Inquiry: 12 00 00 00 60 00
ata1.01: cmd a0/01:00:00:60:00/00:00:00:00:00/b0 tag 0 dma 96 in
res 40/00:02:00:24:00/00:00:00:00:00/b0 Emask 0x4 (timeout)
ata1: link is slow to respond, please be patient (ready=0)
ata1: device not ready (errno=-16), forcing hardreset
ata1: soft resetting link

After unplugging the IDE DVD both from power and data, XP boot times became low again!
It is strange that the drive was fully working in all operating systems, despite delaying the boot time a whole lot.

Side effect of this is that BIOS is stalled for a long time while it looks for IDE devices, which is weird considering I am only using the hard drive as IDE Primary Master. Which makes me think that something is wrong with the cable... or worse, the motherboard. Hopefully the latter. It could also be the IDE/SATA mode, in my case its Compatibility Mode - Primary IDE + SATA (the secondary IDE channel is disabled in this mode). But since 98 does not boot in the "native" (AHCI?) mode, I am not having a lot of options here.

I'll hope for the best as I replace the cable.

XTac wrote:

Side effect of this is that BIOS is stalled for a long time while it looks for IDE devices, which is weird considering I am only using the hard drive as IDE Primary Master. ...

Check if the HDD has a separate jumper setting for "single" or "master without slave" mode. See this example for WD drives.

The best way, of course, would be to put only a single drive on each IDE channel. What I understand is that you can only get both IDE channels working in 'Native' mode, but 98SE does not boot in this mode? Even though it's installed on an IDE drive, and any SATA quirks (AHCI etc.) are not relevant?

Was WinME working in 'Native' mode? If so, I would suggest to look more into the issue of 98SE. Anything is better than having two drives share an IDE channel.

dr_st wrote:

CHKDSK does not run in the background.

Well, yes it does.

Although it's autochk, which is a version of chkdsk that runs if you have an NTFS file system.

To disable, navigate to...

HKEY_LOCAL_MACHINE\System\CurrentControlSet\Control\Session Manager\BootExecute

Look for...

autocheck autochk * /r\DosDevice\C:,

Change to...

autocheck autochk *

Matzo wrote:

dr_st wrote:

CHKDSK does not run in the background.

Well, yes it does.

Well, no it does not. The keyword here is 'background'. When Chkdsk runs at startup on XP it always shows its nice blue user interface so it cannot be unnoticed.

It always runs in the 'foreground' so you can always know that Chkdsk slowed down your boot process. It cannot happen that your boot process lasts 2 minutes and while you are staring at a black screen (as OP described his problem) without any feedback Chkdsk secretly scans your drive causing boot time issues.

My understanding is that autochk.exe fires off in the background everytime the computer is restarted and is this utility that checks the dirty bit on a disk and then runs a chkdsk /f depending on whether or not that flag is set however, on execution autochk has been known to encounter problems and just sit still for a period of time (resulting in boot delays, confirmed that it is autochk.exe via the event viewer) or in other cases just freeze or does run, firing off a check then just looping or doesn't or is unable to re-set the flag on completion.

Matzo wrote:

My understanding is that autochk.exe fires off in the background everytime the computer is restarted and is this utility that checks the dirty bit on a disk and then runs a chkdsk /f depending on whether or not that flag is set however, on execution autochk has been known to encounter problems and just sit still for a period of time (resulting in boot delays, confirmed that it is autochk.exe via the event viewer) or in other cases just freeze or does run, firing off a check then just looping or doesn't or is unable to re-set the flag on completion.

Well, that is interesting, and I could indeed find some references to it happening, e.g., here:
https://www.sevenforums.com/performance-maint … ue-autochk.html

The issue has been solved.

As i suspected, the cause was my DVD drive. For some reason it delayed the boot sequence of every operating system i threw at it, despite the fact that it worked pretty much flawlessly once an operating system was running. After swapping the drive, the issue disappeared pretty much immediately.

Thank you for all advice given here.