I *think* I have things working now, here's what I did thanks to both hclarkjr and Thorin, I updated the BIOS to v1006 Beta 5. It didn't seem to work at first, but then another post in the newsgroup pushed it the extra edge, allowing me to enable DMA on both drives (although I want to find something to run some benchmarks just to make sure, any suggestions?).
Here is something that people with similar problems will most likely find useful:
> The information in this article applies to:
> Microsoft Windows 98
> Q235859 - DMA CD-ROM Drive Icon Does Not Appear in Windows Explorer
> -------------------------------------------------------------------------- --
> ----
>
> SYMPTOMS
> When you try to view a CD-ROM drive in Windows Explorer that requires Direct
> Memory Access (DMA), the drive may not be present, but the drive may be
> present in Device Manager. If the DMA settings are disabled in the CD-ROM
> properties, the drive may be present after you restart your computer,
> although a CD-ROM drive that supports DMA may not retain the DMA setting
> after you restart your computer.
>
> CAUSE
> This problem can occur because during enumeration of your hardware devices,
> a device conflict can occur, and this may cause Configuration Manager to
> rebalance the resources of your computer. During this arbitration process,
> the Integrated Drive Electronics (IDE) controller input/output (I/O) range
> is changed from the boot configuration to a different configuration, but the
> primary and secondary controller resources are not changed properly.
>
> RESOLUTION
> To resolve this problem, perform a forced configuration of the hard disk
> controller:
> 1. Click Start, point to Settings, click Control Panel, and then
> double-click System.
> 2. Click the Device Manager tab, and then double-click the Hard Disk
> Controllers branch to expand it.
> 3. Double-click the listed IDE controller.
> 4. Click the Resources tab, and then click to clear the Use Automatic
> Settings check box.
> 5. Change the I/O range from the current setting to a different I/O range,
> and then click OK. For example, if the setting is currently 1410-141f,
> change it to 1060-106f.
> 6. Close all open Windows, and then restart your computer.
>
> STATUS
> Microsoft has confirmed this to be a problem in Windows 98.
Once that happened and I rebooted, DMA stayed checked in both CD-Drives, thanks again for the help!