A common problem is having the same disk drive listed twice, here's how to fix the problem
While researching a problem at Seagate's SeaTools forum, I ran across a post about disk drives showing up twice in the SeaTools disk diagnostic utility. The post presents a scenario in which the same disk drive is listed twice, yet the utility acts on only one instance of it. I've seen this "double vision" scenario before with another disk utility. Apparently, it's a common problem in disk utilities.
To fix the problem, open up Device Manager (devmgmt.msc) in Windows and select Show hidden devices on the View menu. In the devices tree, expand Disk drives. Notice that some of the icons are a light gray (i.e., grayed out), whereas others are a dark gray. Make sure you're able to differentiate between those that are grayed out and those that are the dark gray. You might need to run your display adapter's adjustment software or manually tweak your display monitor's settings to see the difference between the light and dark gray icons.
Some of the icons are grayed out because they're for removable drives that currently don't have anything inserted in them (e.g., drives for USB flash sticks). Some of the other grayed out icons will have the same name as disks you know are currently attached. Don't do anything to the dark gray icons. Instead, right-click the grayed out icons and select Uninstall. You'll get the message Warning: You are about to uninstall this device from your system. Click OK. (Note that it won't hurt anything to uninstall grayed out icons for items such as USB flash stick drives because the drives will be automatically reinstalled the next time you insert the devices into the computer.) Finally, run the disk utility again. You shouldn't have the same drive listed more than once this time around.
Based on my experience, drives become grayed out (i.e., orphaned) when the drives are removed and when disk controllers or disk controller drivers are changed. I've seen this happen when changing the BIOS Serial ATA (SATA) boot drive from IDE mode to Advanced Host Controller Interface (AHCI) mode. I've also seen this occur after running vendors' driver packages, such as the Intel Rapid Storage Technology Driver package and the older Intel Matrix Storage Manager Driver package.
Let's run through an example. I changed Windows 7's native SATA AHCI driver to Intel's ICH9R SATA driver. Figure 1 shows the IDE ATA/ATAPI controllers branch after this change. As you can see, uninstalling the Microsoft controller driver left five orphaned icons (i.e., ATA Channel 0 through ATA Channel 5). Note that you can still see the valid dark gray icons for ATA Channel 0 and ATA Channel 1. (This particular motherboard has two controllers.) Figure 2 shows the IDE ATA/ATAPI controllers branch after I "uninstalled" the five orphaned icons.
If you plan on uninstalling all the orphaned icons in the Disk drives and IDE ATA/ATAPI controllers branches of the devices tree as part of a spring cleaning mission, you might also want to do some spring cleaning in the tree's Storage Volumes and Storage volume shadow copies branches. However, you need to be very careful in the Storage volume shadow copies branch because each valid icon shows a light gray volume on top of a dark gray volume. The orphaned icons show a light gray volume on top of a light gray volume, as shown in Figure 3. The valid icon entries are created when a restore point is created. I'm not sure why the orphaned icons exist. Figure 4 shows the Storage volume shadow copies branch after I "uninstalled" the orphaned icons.
I haven't experienced any noticeable performance increases or improved OS startup times by uninstalling orphaned icons. (However, I haven't clocked it to determine before and after statistics.) As far as I can tell, the cleanup simply removes the orphans from the disk utility software and releases registry space for reuse in the Windows System registry hive.