That's strange. I feel that if it was really the fault of the IDE controller, Windows wouldn't want to install/boot up at all. The reason why I say this is because for things like SCSI cards that Windows doesn't have drivers for, you need to install the drivers for them during setup to be able to use the HDD (i.e. in Windows NT4 setup, you would manually have to insert a driver disk after it tried detecting any controllers so that Windows could be installed). I'm not sure how Windows 98 handles things like that, however.

What make/model is the CD-ROM drive? You might be able to try temporarily installing something like Windows 2000 or XP to see if the CD drive shows up in those versions. An even better option might be to try and install the CD drive into another vintage system (if you have one), and install Windows 98 on that, and see if it shows up there.

Another thing you can do is switch up the positioning of the drive. If it's the master drive of either the primary or secondary IDE port, you could try switching it to the other port, or try making it a slave drive to the port that the HDD is on, and configuring the HDD to be the master drive. As a general rule of thumb, I always make the HDD the primary master drive, and use the CD drive as a secondary master. Sometimes, if the jumpers on the drive are wrong, the drive won't even show up on BIOS setup (for example, if your drive is the only drive on that port, and you have it jumpered to master). I've been fooled by this a couple of times and have had no idea what was going on until I looked into it. This might be a case similar to yours, albeit, it shows up in BIOS and works, but doesn't work in Windows.

You might need to try and get multiple versions of the chipset driver online and go through each one until you find something that works. That's all I can think of at the moment.

Thanks for the reply. The drive is a NEC cdr-1800a 24x drive. I will mess around with it seems more. I just couldn't remember if Windows 9x required DOS drivers to be loaded for a CDRom to be visible? I know if I boot off a floppy worth CD support it functions just fine.

Just an update, I noticed in device manager that the hard drive nor CDRom show up. I was almost certain that my hard drives have always showed up there on past win 9x systems. The only way I have been able to get the CDRom to work is through using msdos driver install from NEC. I am almost certain this is an issue with the IDE controller. I can't find a driver for it mornuo to date than what Windows 98 installed by default. I am at a loss here.

Did you use Ontrack or such?
These problems are just normal if one uses this.

Perhaps it really is a chipset issue. I.e., the HDD and CD-ROM aren't visible to Windows 98, since to it, no known PCI IDE controllers are installed in the system.
However, at the same time, both devices do appear on DOS, because the BIOS provides a working int13h interface for this strange IDE controller.
If you can, check the BIOS setup for IDE or PCI/ISA IRQ settings. If possible, try different settings. Switch between ISA IDE (Legacy IDE) and PCI/Bus Master IDE,
assign IRQs for a classic IDE controller (IRQ14/15). Also try changing "PnP aware OS" and try different ACPI levels (or disable it and use APM).
https://www.webopedia.com/quick_ref/IRQnumbers.asp

Have you tested if it appears in the DOS prompt? That should tell you if it is working at least. If it doesn't appear, I would try a reinstall. Reinstalls are a normal part of life when working with Windows 9x, 🤣

Also, have you tried locating online drivers for the IDE controller separately from Packard Bell? Maybe if you find a different version it would work?

Most people don't do this, but it is useful:

use the lastdrive=z option together with the MSCDEX /L:n option, using another than the default drive letter

This way you can use the DOS CD driver and the Windows driver concurrently, with Joliet long filename support.
D: appears as the Windows CD driver and the other letter is the DOS version.