Are you running XP? If so, then be sure to disable indexing. Indexing keeps track of the files that are accessed most frequently. When the PC is not in use, XP then rearranges the hard disk and moves these files to the front. It will continuously do this...
go to Services under Administrative tools
stop the Indexing service
disable the Indexing service
go into windows explorer
double click your C: (or whatever your main is)
once open select all
select all hidden if it prompts you to
right click all selected files
choose properties
choose advanced
uncheck the "For faster file searching, allow Windows to index this folder"
apply to all subfolders and files
It was explained to me that not only is this service used for searching, but also for system performance enhancement. I noticed that I would defrag my drive with Norton, and the next day it would be all fragmented again. I had done nothing on the PC except leave it on overnight. Ever since I have done this, my drive remains optimized and Norton is happy...
If I am way off on this one, somebody please correct me because it wasnt a Micro$oft engineer that told me this one!
...hope this helps?