You could always install the OS to the CF with a USB adapter, then transfer to your CF adapter. FWIW I use 3x Startech IDE-CF adapters on 3x different old PCs and never had an issue.
https://www.amazon.com/dp/B000T9QQP0

Lylat1an wrote on Yesterday, 05:00:

I'm having trouble installing Windows 98 SE onto CF cards. […]
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I'm having trouble installing Windows 98 SE onto CF cards.

It works without issue through an IDE to SD card converter, but for some reason using a removable "native IDE" SSD gives me errors each time.

I'm using SanDisk Extreme CF cards, I figured they'd be high enough quality.

The CF adapter is an Adtron model for a 3.5" bay.

I have had issues with drive geometry not being auto-detected properly sometimes on CF cards. You may have to mess around with that in the BIOS to get the cards to work properly. Keep in mind you'll need to delete all the partitions if you change how the BIOS sees the drive.

Also, along those same lines, I have run into situations where partitioning and formatting on a different system didn't "fit" the geometry that the intended (usually older) system would try to use, so even though the drive showed up okay it would get screwed up when being written to.

Ozzuneoj wrote on Yesterday, 15:12:

Lylat1an wrote on Yesterday, 05:00:

I'm having trouble installing Windows 98 SE onto CF cards. […]
Show full quote

I'm having trouble installing Windows 98 SE onto CF cards.

It works without issue through an IDE to SD card converter, but for some reason using a removable "native IDE" SSD gives me errors each time.

I'm using SanDisk Extreme CF cards, I figured they'd be high enough quality.

The CF adapter is an Adtron model for a 3.5" bay.

I have had issues with drive geometry not being auto-detected properly sometimes on CF cards. You may have to mess around with that in the BIOS to get the cards to work properly. Keep in mind you'll need to delete all the partitions if you change how the BIOS sees the drive.

Also, along those same lines, I have run into situations where partitioning and formatting on a different system didn't "fit" the geometry that the intended (usually older) system would try to use, so even though the drive showed up okay it would get screwed up when being written to.

That sounds plausible in my situation.

Though I wonder why it doesn't occur with my SD Card adapter?

Lylat1an wrote on Yesterday, 20:56:

Though I wonder why it doesn't occur with my SD Card adapter?

This is my current understanding of the situation:

1. IDE-SD adapters use an FC1307A IDE-to-SD chip and so long as that chip is compatible with your system's IDE interface, it does not matter what SD card you use. The main downside of these is that like other forms of flash media they do not support Multiple Sectors Per Interrupt, and the transfer rate is slow enough that a late spinning IDE drive easily outperforms it.
2. CompactFlash cards are touted as "just IDE through a passive adapter" but this is dubious; compatibility is highly specific to the card. They may randomly ground things like IOCHRDY or DALE causing chaos when connected to an ISA Multi-I/O card. They may randomly refuse to work as "slave" and only as "master" (in my case, doing ATA IDENTIFY against a 512MB Transcend card when it is in the middle position of the cable as "slave" with an HDD connected as "master" at the end, has bits flipped in the response in different positions on each attempt). In a Discord conversation, someone suggested to me that the issue is that CompactFlash cards claiming to be 5V-tolerant actually vary greatly in their 5V tolerance when looking at the data lines using an oscilloscope.

jakethompson1 wrote on Yesterday, 21:10:

The main downside of [IDE to SD] is that like other forms of flash media they do not support Multiple Sectors Per Interrupt, and the transfer rate is slow enough that a late spinning IDE drive easily outperforms it.

This is why I wanted to use CF over SD.

I'm going to attempt specifying the drive type from AUTO to USER on my CF card, and see if things go better.

I have been having similar issues today trying to use recently bought supposedly industrial Transcend CF cards. I think the 512mb ones may be fake and corrupt data. The 2gb ones, from another seller, seem to be the claimed capacity but my target PC (a 386) doesn't understand anything bigger than 512Mb or so. I haven't had any luck on the 386 so far with larger new cards. But a used Cisco 64mb one works perfectly. Ideally I want to max out the storage on the 386.

RetroPCCupboard wrote on Yesterday, 21:57:

I have been having similar issues today trying to use recently bought supposedly industrial Transcend CF cards. I think the 512mb ones may be fake and corrupt data. The 2gb ones, from another seller, seem to be the claimed capacity but my target PC (a 386) doesn't understand anything bigger than 512Mb or so. I haven't had any luck on the 386 so far with larger new cards. But a used Cisco 64mb one works perfectly. Ideally I want to max out the storage on the 386.

If you haven't already, you might clip the IOCHRDY and DALE pins on the adapter and it might improve compatibility. Plucking certain IDE pins for better CF-IDE compatibility

Lylat1an wrote on Yesterday, 21:19:

I'm going to attempt specifying the drive type from AUTO to USER on my CF card, and see if things go better.

Yes, try "user" modes instead of auto, and choose LBA mode.

It was also necessary to disable UDMA modes for that IDE channel on some of my motherboards/BIOS.

SanDisk web page for these cards or data sheet doesn’t mention anything if these cards have True IDE mode or not. If it is not mentioned at all, I’d expect it not having it.

If it doesn’t have one, it isn’t surprising the cards won’t work with your typical passive CF adapter.

Fazeshift wrote on Today, 02:51:

Lylat1an wrote on Yesterday, 21:19:

I'm going to attempt specifying the drive type from AUTO to USER on my CF card, and see if things go better.

Yes, try "user" modes instead of auto, and choose LBA mode.

It was also necessary to disable UDMA modes for that IDE channel on some of my motherboards/BIOS.

I tried, but I forgot that I was using an add-in card for my IDE ports that's much faster that the onboard ones.

The card's detection process is automatic, and doesn't have a prompt to configure things manually.

Lylat1an wrote on 22 minutes ago:

Fazeshift wrote on Today, 02:51:

Lylat1an wrote on Yesterday, 21:19:

I'm going to attempt specifying the drive type from AUTO to USER on my CF card, and see if things go better.

Yes, try "user" modes instead of auto, and choose LBA mode.

It was also necessary to disable UDMA modes for that IDE channel on some of my motherboards/BIOS.

I tried, but I forgot that I was using an add-in card for my IDE ports that's much faster that the onboard ones.

The card's detection process is automatic, and doesn't have a prompt to configure things manually.

What card are you using? Most have some way to configure them because this was often necessary back in the IDE days.