If your DVD-Rom is sharing the IDE cable with another device, be sure your jumpers, if any, are set correctly. If one drive is jumperless, make sure the other is set to slave.
In addition, if you are sharing this drive with a burner, you may have to isolate the drive on the IDE cable. Try routing the second drive on the same IDE as the Hard Drive. With the DVD on an isolated IDE, your problem should go away.
Some burners don't work well with others on the same IDE cable.
You may be thinking, "Well, it always worked before." I can tell you that I have repaired many PC's with issues like this with the above mentioned fix. Most notably, a drive will be listed under "My Computer" after system boots, the next time the computer boots, however, the drive may or may not be listed. It seems to be random.
Hope this helps.