losing files from server - Server 2003

We seem to be missing files from a Server 2003 on a Dell 2950 server with 4 gigs of Ram and Xeon processor.  Since we are out of warranty and can't get any funding for this, we need to somehow resolve this issue.  I've ran process monitor and all three default views:  Pages/sec, Avg. Disk Queue Length, and % processor Time seem to be a bit high at any given time.  We did see an alert from SCOM stating the following:  

The threshold for the Logical Disk\Avg. Disk sec/Transfer performance counter has been exceeded.

We're thinking that it may be a disk issue, but can't confirm at the moment.  We're planning on installing some updates from last week and then rebooting the server.  Would we be able to view any issues at this time?  If so, how?  We wanted to do somekind of diagnostic on the server.  I'm presently installing Openmanage, but never used this utility before.

We're also running a virus scan on the server as well.

Help!
uppercut71412Asked:
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Seth SimmonsSr. Systems AdministratorCommented:
as far as ruling out any hardware issues, installing open manage is a good start so you can see hardware status

here are diagnostics you can run

http://downloads.dell.com/FOLDER01456532M/1/dell-onlinediags-win32-2.30.0.70.exe
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ZabagaRCommented:
If you're missing files I'd run a chkdsk c: /f /r
I'm assuming C:\ but run it against each drive on the server.
It will probably tell you the disk is locked and in use, then ask if you want to run chkdsk at the next boot up.  So say YES to run at next boot-up then reboot the server at your earliest convenience. Do this process for each disk. I wouldn't run chkdsk on more than 1 disk at a time. It's only worth running a defrag on your disks too.
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uppercut71412Author Commented:
I ran the online Dell diagnostics and everything returned with no errors to report.  I think we are good as far as hardware.  We might need to setup sometime of audit to show anytype of deleting/moving files/folders from a user perspective.
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uppercut71412Author Commented:
Any thoughts?
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uppercut71412Author Commented:
great answer
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Windows Server 2003

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