Okay, my thoughts are that it's either bad IDE drivers (try updating them if you haven't done so yet) or at least one of your hard drives is acting funny. (Try running a thorough scandisk to get a surface scan for any errors, and if nothing comes up, try a defrag.)
Of course, one must also wonder what actual hard drives you are using...
<font color=blue><pre>If you don't give me accurate and complete system specs
then I can't give you an accurate and complete answer.</pre><p></font color=blue>