The symptoms you describe could be caused if you had the IDE ribbon cable plugged in backwards. Do you have the 1 pins alligned?

There are also some BIOS from that period that fail when they see storage devices with more than 65535 cylinders. See if there is a bios upgrade for your motherboard or configure the CF to have < 65535 cylinders in your BIOS.

CF adapters dont have any more logic in them than a 40 pin to 44 pin ide adapter. They just take the 40 ide pins & power to the 50 pin connector of the CF and takes one of the pins to ground so the CF knows it needs to act like an IDE device. If there is an incompatibility, it would be in the CF or motherboard. Unless your CF adapter is just broken. I did get a package with a pair of broken adapters recently. Some of the pins were floating. So that’s not so much an incompatibility as it was poor quality control.

In addition to what douglar mentioned, I would also try the following:
1) put the CD-ROM on primary IDE by itself (and set as master.) Do not connect the IDE-2-CF adapter. With that, see if the motherboard detects the CD-ROM.
..a) if not, you have problem either with the IDE cable that's connected to your primary IDE channel or with the circuitry of the primary IDE channel on the board.
..b) if the motherboard does detect the CD-ROM on Pri. IDE, what happens if you connect the IDE-2-CF adapter as slave on the same (primary) channel? If same issue, try connecting the IDE-2-CF adapter on secondary IDE ch. as master. This will verify both your IDE cables and the two IDE channels on the board.
2) remove the gotek floppy emu., disable floppy along with the serial and parallel ports (+ any IR headers too), and etc., just to keep things more simple. Maybe for whatever reason, there is a weird IRQ conflict going on.

If just plugging in the adapter without any CF card in it is causing the hang, then it's a faulty adapter.
If the issue happens only when putting a CF card, then it could be one of many reasons, as others have said:
* BIOS doesn't like those particular CF cards. Try other ones of smaller size maybe. Or update BIOS to latest in hopes it improves support.
* Incorrect connection of adapter to the IDE connector (flipped).
* Many CF cards don't like anything else on their IDE channel. So don't put any slaves on their IDE cable, and keep the adapter jumper on Master.
* Not providing power to the adapter, but this is not your issue. Also, some small size CF cards don't even need it.

My bet is the CF cards themselves are too large for your BIOS. Find smaller sized ones or try the BIOS upgrade if you are brave enough.

Managed to get this working. I updated to the latest BIOS and also put a 80 wire cable.

However noticed a new issue, not sure if its related to the CF Card, way its partitioned or not.

Have a 32GB Sandisk Extreme UDMA 7 CF Card. If I plug that in, machine hangs, wont boot. If I plug in an older 4GB Sandisk Extreme III CF Card, it detects the drive straight away.

Any thoughts? Are there any CF cards just not compatible with this motherboard? OR do i need to format it or set it up differently? Or should I just get some more of the older CF Cards?

Yes some mobos are like that unfortunately. They can't even POST if you connect a too-large HDD to it. How large? That depends on the mobo. I have some 486s that refuse to post for anything larger than 504MB.. you can't even get to the BIOS or have the chance to run a disk overlay software.

So yeah, try with different CF cards. But expect that some will fail like that...