In my case server was running on Windows Server 2003, and on every reboot check disk was triggered. The reason for this kind of behaviour was that disk drive D: was marked as dirty, and chkdsk was never ending the tests on restart. You can check if the drive is marked as dirty using fsutil :
Marking the drive as NOT dirty, can be done using chkdsk /r.
D:\>fsutil dirty query d:
Volume - d: is Dirty
Marking the drive as NOT dirty, can be done using chkdsk /r.
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