Just some questions first. If you have the disk in the drive, but do not access the disk, does it shut down the same way?
Do you close down all your programs before you shut down? If a program thinks a file from the disk has been changed, it will want to save the changes in the file.
Try disabling any checking programs like Antivirus or Antispyware before shutting down and see if there is a difference.
You mention that the disks cannot be read sometimes. Try using a different brand of blank disk. Look for a firmware update for the drive.
You mentioned the drivers, the drivers involved would be IDE
Controller drivers and/or the chipset (motherboard) drivers.
Do you happen to have Nero, and in particular, InCD installed? That can cause headaches sometimes.
If you use DVD-R disks, it might prefer DVD+R or visa-versa (check the recommendation for the drive at the manufacturer's website). It might also be a problem if the disk is not "finalised".
Look for any "drive" programs that might be installed. Programs for running some flash/micro drives can cause problems.
Do you have any form of file encryption enabled?
Mmmm, see what happens by going into Safe Mode and accessing the disk. Is it reliable, etc, there?