Most of those files have been marked as Excess Allocation.
This is from http://www.execsw.co.uk/home/html/home/diskeeper/faq.htm#q7
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What does "Excess Allocation" mean?
The file is one that is being held open by the kernel. In addition it is being written and rewritten on a regular basis by the kernel. At some point in its lifetime, it WAS large enough to require 2 extents' worth of allocation. However, since then it was rewritten from the beginning with less data AND NEVER CLOSED. Since the file is being held open, NTFS figures it might have more data written into it at some time in the future and doesn't release the extra allocated clusters...leaving them assigned to this file for possible future expansion. The excess clusters will be r
eleased when the file is closed, which, unfortunately, will be the next reboot.
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I believe Exec are working on a fix for this...
As to why when you have rebooted several times it has not cleared, I don't know.
Also, since these are NI files, they are not in use all that often, and I don't think you'll notice too much performance issues.