My guess (based on what you're telling me) is that you have a hardware (or at least a file system) issue.
Boot from the Server 2008 install disk and use the “Repair your computer” option. It'll give you three options including Command Prompt.
Use that to run a CHKDSK and see if it thinks anything is up with the file system. If it says there is, then you'll want to rerun CHKDSK with the repair option(s) switched on (usually /F, might be different in the 2008 repair console you'll be going into via the DVD, so do a chkdsk /? to figure out what the exact switch options are).
If that doesn't help I'd say next test the hard drives by using the manufacturer's diagnostics, and if that comes up clean then start testing the memory using Memtest86+ (for a day or more, we usually aim for 72+ hours of continuous memory tests before we claim it's 'OK').