Your CD-ROM may require a seperate driver to be loaded.
It might be loading using a generatic one on either a bootable CD or bootdisk to load Windows 98, but require a driver for W98 once your OS is loaded. Upgrading to XP would probably solve this. but would cost you $ as well.
Look in the device manager and see if it detects the device and also verify it see’s it still in the Bios as the PC boots on the IDE cable.