The Pioneer's tend to work best as a master drive. Some older CD-Burners have the same problem. The CD-ROM shouldn't care where it is, so long as it is properly jumpered. For safety sake and speed, it would be best to have the HD by itself as Master. This prevents any potential slow-down on the channel from the optical drive. The channel will throttle down to the slowest drive's speed if both drives are active. Ripping a CD or playing a game from the CD will slow down the HD performance if they are both on the same channel. Isolating the HD insures optimum HD performance all the time. Put the Pioneer and the plain CD on the same channel and set the Pioneer as Master or Cable select--make sure it is at the end of the chain. If the CD-ROM is not DMA capable (the BIOS reports it is in PIO mode) do not put it on the same channel. Reference the same problem with the HD. If that PCI card is an IDE controller, put the remaining drives there, again making sure the writer is in the end connector and jumpered as Master or Cable Select. If you don't have an add-in controller, you might want to shop around for one. You can easily find them for under $30 US online, $50 in store. If you don't/can't do this, then it would be best to retire the plain CDROM and use the burner as secondary to the DVD on the same channel.
If it ain't broke don't try to fix it! But, hell if you can tweak that bastard just a little bit more....hehehe.