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It may be the difference in whats its comparing. Its likely comparing the number of files in your hard drive that windows says there are with the number of files its allowed to look at. Windows reports hidden files and folders in the first number, but it probably doesn't let it index hidden files. So, the more other files you have, the higher your percentage. If you have a fairly new windows system, you have almost 16,000 windows files to your system's. On my newest computer (6 months) I have 40,000 files non-windows and that includes the documents and setting folder that has hidden files and folders.
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