You write "that Windows performs a check disk at boot". Normally this only happens if you did not shut down the system correctly. The drive has the status "dirty" then. So why does your system not shut down correctly? Just switched the power off and no correct shut down? Check the Event Log for other reasons.
Perhaps you should run chkdsk from within the OS to check if the disks are really clean. If you find errors check the S.M.A.R.T. data of your disks. You also could run a HD surface scan (HDTune for instance can do).
Thanks for the reply. I got the following from the event viewer. The problem started last week, january 3rd during system boot up.
This NTFS warning shows up 3 times without any prior error.
The file system structure on volume C: has now been repaired.
30 minutes later, the NTFS errors shows up 3 times
The file system structure on the disk is corrupt and unusable. Please run the chkdsk utility on the volume \Device\HarddiskVolume2.
the day after, the same NTFS error has repeated every 1 minute for a full day
followed every 5 minutes with this Service Control Manager Error:
"The Multimedia Class Scheduler service entered the stopped state.
The Multimedia Class Scheduler service entered the running state.
I am having the user run a manual chckdsk today to see if there are any futher issues with the disk. The user indicated that one he had to force shutdown the machine because Excel crashed and Windows wouldn't shutdown. Like I said, the other computer we have setup the same way also suffers from the dirty drive problem. Is a RAID setup more prone to getting dirty drives than a regular AHCI setup? At this point I doubt that both machines have bad drives but I will run the checks anyway as you mentioned.