I encountered a similar problem where the CDROMs would disappear but Device manager did show that there was a problem. I had tried refreshing drivers, swapping cdroms...ended up reimaging the 1st i saw it. Finally looked it up and found this article: http://support.microsoft.com/default.aspx?scid=kb;en-us;320553
Basicly there is a reg key you have to delete. Goto HKEY_LOCAL_MACHINE/System/CurrentControlSet/Control/Class/{4d36e965-e325-11ce-bfc1-08002be10318}
and delete the upperfilters and lowerfilters entries. Should be REG_MULTI_SZ data types. I only had the upperfilter showing and removed it, rebooted and the cdrom was working normally afterwards.
Might give this a try.
AS ALWAYS...Working with the registry can be dangerous. You may want to back up the registry or at least the Reg key here before making changes. That said I have not had any problems(yet) deleting the upperfilters entry.
hth,
Jason