Go to the device manager and go to the properties of the CDD and you will see you can reserve a letter for it forcing the second HDD to take a later letter. maybe this got selected for some reason.
Win98 has the drive letters assigned the same way they are in DOS: HD0 primary = C, HD1 Primary =D, HD0 extended/logical = E, etc. The CD gets assigned a drive letter by Win98 since DOS has no inherent support for CD’s. WinNT/2K/XP can assign drive letters any way you want.
Try this: force the CD to a lower drive letter, like F. Reboot and see what your second HD letter is. If it’s where you want it then force the CD to letter E.
If nothing else works, go to start->settings->control panel find the System icon and under the hardware tab delete the CDRom and/or the d: drive hard drive. I don’t think you can delete the C: drive unless you boot in safe mode, but don’t delete it anyway.