You're right Bob I have experience with Desktop OS's, viruses, etc. This experience is perhaps coloring my thinking. Only the owner and myself have access to the server. No one surfs with it, it's just a server with 12 clients.
Why was I asking about running SFC? Because so many things are not accessible, reminds me of a desktop that has had a rootkit change permissions and settings. For example, I can get to control panel, in details view lets say...but the first four items listed do not have identifiable icons, they are the Windows generic "I don't know what these are" icons and no text adjacent to them, the rest of the icons are there with text descriptions as normal. When I select add/remove it doesn't populate the list. So I can't look to see what updates have been installed. When I first logged on I was able to get add/remove to populate. In fact I removed software Yahoo Toolbar, Yahoo updater, Freeze.com, and some PC registry fixer that were not there a week ago. Ironically the owner has a Yahoo account and swears he hasn't downloaded anything. He also accesses the server from home with VNC mapped to a higher port, not 5900. Some things lead me to believe it may be viral or malicious, again desktop os experiences may be swaying this opinion.
The reason I was questioning the RAID condition is that the server will hang for a minute and eventually repaints the screen. For example when logging in, what icons are left on the desktop take way too long to display. Or I can click on something, with task manager up and see little if any CPU activity and then suddenly the machine catches up with the clicks. I've seen this in the PC desktop world when a drive has bad sectors or crosslinked files. They act really slow, not a lot if any CPU usage going on while it's waiting and then suddenly it's displayed.
Also I can see IE 8 open up in the task manager when I click on it and then immediately disappears from the process list without ever opening on the screen. Tried re-installing it and I get an immediate error after selecting run, install, and check install updates, then it errors "Internet Explorer installation did not complete"
Will try to insert a link to photobucket where I put a couple screen shots. not sure it's gonna work.
<a href="http://s1341.beta.photobucket.com/user/winonawhiley/story/27459" target="_blank"><img src="http://i1341.photobucket.com/albums/o755/winonawhiley/story/27459/thumb/large.png" border="0" alt="winonawhiley's Story"/></a>