I had this type of problem except. Except it was between my harddrive and NEW CD drive (It's just 56x cd drive).
During normal use of the computer, out of no where my D: (80 gig hdd) and my E: (CD drive) would just disappear. I lost access to both of them. I rebooted and it said on the boot screen:
for both of my drives. I went into the bios and it didn't detect them.
I later replaced the IDE cables going to both of them and what do you know, they worked great. They still are working great, too.
This isn't the same problem as you, but they are close. I would recommend replacing any or all cables going to your CD Rom drives to see if something is wrong with them. Mine didn't have any types of cuts or anything on them.
Windows 7 Pro x64
AMD 965 Black Edition 3.4GHz
ASUS Crossfire III
Corsair 650 Watt
Sapphire ATI 5770
500GB Samsung*2 | 150GB VelicoRaptor 10K HDD
C# Programmer+Web Programmer