I was having this problem before on a USB drive, but now it's happening on my main RAID5-backed hard disk:
2013-10-17 9:37 C:\>dir "C:\Shares\Shared\Reference\Safety Management System\Vid
eo CD\AutoPlay\Docs\Manuel*"
 Volume in drive C has no label.
 Volume Serial Number is 3C18-E114
 Directory of C:\Shares\Shared\Reference\Safety Management System\Video CD\AutoP
lay\Docs
2003-09-09  11:29 PM         1,056,768 Manuel d'intervention d'urgence MFC.doc
2004-06-20  10:36 PM           139,849 Manuel d'intervention d'urgence MFC.pdf
               2 File(s)      1,196,617 bytes
               0 Dir(s)  196,068,691,968 bytes free
2013-10-17 9:38 C:\>dir "C:\Shares\Shared\Reference\Safety Management System\Vid
eo CD\AutoPlay\Docs\Manuel d'intervention d'urgence MFC.doc"
 Volume in drive C has no label.
 Volume Serial Number is 3C18-E114
 Directory of C:\Shares\Shared\Reference\Safety Management System\Video CD\AutoP
lay\Docs
File Not Found
2013-10-17 9:38 C:\>
This is from a Command Prompt window where I went to Properties and told it I wanted to modify who it ran as.  I opened it, had it run as me with the "restricted access" unchecked, then ran the above.
The file in question has the following ACLs: Administrators, SYSTEM, and OurCompanyUsers.  All three have full control of everything.  Nobody has any Deny bits set.  I am a member of Administrators.  So I don't believe it's a permissions issue.
It's not a USB drive, so this time there is no question of USB hardware.
Windows Server 2003 Standard Edition SP2.
What does this mean?  Is this more likely a hardware or software problem?