Mmmh that's very strange, but sounds more like a hardware issue and not a problem of the system, please check this (just written) howto: How to check and verify that your computer doesn't have hardware problems
If you don't have these problems, we must check what is causing it (i still convinced that is a hardware problem, probably by the hard disk in a "sleep" state)
Try to run "dmesg" when it happens to see if you have any useful info
