Your package database and your installed packages are out of sync. I cannot tell you why, but I can at least tell you what I see here.
I misinterpreted what I saw in the cvs log for bzip2's Makefile, because August 9 2010 was the build date for the i386 bzip2-1.0.5 package for 4.8-release. Therefore, some of these existing files are from that package.
The i386 package for bzip2-1.0.6 for 4.9-release was built February 16 2011, and none of them are on your system.
You have some files dated November 16 2010, source unknown.
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If it were me, I would make a clean install of the OS, since something has occurred that caused this inconsistency. As to root cause, I would look to administrative changes you made a year ago, or any installs/deinstalls at that time.
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