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NTFS...... How reliable is it?

I have multiple drives and without stopping window unexpectedly or doing anything other than normal turn on and shut down procedures I have been loosing files or having files be rendered useless. In many cases the system will discover a drive "bad" and perform a scan and repair on it at boot up time. Why is this happening. I ran Norton Anti Virus to check if any virii existed on them. Nothing was found. One unusual item was; most times if I went into a folder to view files then I stepped back out of the folder and then attempted to delete it I would not be able to as the system said the folder was in use by another progrm. I could delete that folder or any other folder if I never jumped into it or if I just booted my system. I am at a loss as to what the problem is and what to do over this. My drives I am talking about are my Maxtor 200GB drive and Hitachi 120GB drive on my pentium system. Motherboard is P4P800. Any suggestions?
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