Three Database Files Appear & Root Directory Icons Rearranged

I recently upgraded to Mountain Lion (10.8.5) from Lion on two of my Macs (15" MBP, Late 2011 & iMac 20" Early 2008). On both machines, seemingly at random, three database files appear on the root directory (sorry I can remember the names now) and all of the files/folders on the root directory are rearranged in alphabetical order. I have not been able to determine what triggers this action, but it is really annoying having to rearrange all of the file icons.
Anyone have an idea what might be causing this and how it can be "fixed"?
Thanks!
Gordon

Have you found an answer to this problem? I have found it happens in Safari > Preferences > Privacy. When you click on the Privacy icon header, instantly the 3 .db files appear and re-arrange all my files into alphabetical arrangement on my root directory (Mac Pro SSD). It will also behave this way when you choose "Reset Safari" from the drop down Safari menu.
Regards,
Haydude

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