It is my belief that you may have a damaged package database (/var/db/pkg/*) beyond this one file. I say this because if I've understood what you've posted, after running diff to compare the files you edited the file in the database and the problem still remained. If that is so, replacing the file would not work unless you edited the file incorrectly.
As you have a second system that is also showing packing list issues, there may be something you are doing procedurally that is damaging the package databases (/var/db/pkg/*) on your systems. This is just conjecture, and if it were true I do not know what you might be doing to cause it.
Last edited by jggimi; 7th April 2012 at 09:40 PM.
Reason: typo, clarity
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