We have an old Windows Server 2003 R2 that we still haven't quite phased out yet.  It has a few roles that are being moved but not just yet.  We have been having some issues with the system and it seems like we need to run checkdisk quite frequently on the system to keep it more stable until lately.

Lately, however, checkdisk has not been coming up clean.  Until the last week or two, I had to run checkdisk (with fix option) about 3 or 4 times on reboot and eventually the last one came up clean.  Now I have restarted up to 6 times with checkdisk (fix option enabled) and it still comes up with errors.  I have checked the Dell PERC 6/i and it does not show any problems on the hard drives.

The only way I was able to tell what the problems are with the hard drive is when I used VMware Converter to make a virtual machine out of the hardware.  Running VMware converter, I found that there is a a warning - Unable to read the block at offset "223,909,376" on volume 'C:' and the worst part was there there was another error at the end of the VMware image.  The second error is "Windows - Registry Hive Recovered" and it reads out that the "-----\WINDOWS\system32\config\SOFTWARE was corrupted and it has been recovered.  Some data may have been lost."  This is my biggest concern.

How do I go about addressing these potentially bad sectors on a RAID-1 configuration of two WDC WD2502ABYS-18B7A0 hard drives using a Dell PERC 6/i controller?

Do I follow through with a virtual version of the server to get me by for the time being or is there a better solution to fix the problems with the physical machine while phasing out the machine in the next few weeks here?