Cs5 font tracking mystery

In our prepress workflow we have a default set of folders for every job:
Main Folder:
     -art
     -old fonts
     -docs
          -Document fonts (inside docs)
     -customer files
     -impo
Anyway, here is the wierd part.  If I load the font into suitcase fusion from the Document Fonts folder, I get one set of tracking.  If I load the font into suitcase fusion from the old fonts folder I get different tracking!  This is on a mac running mountain lion.  I have never seen this before, and I can't figure out why, the contents of both font folders are identical.
Note the where the second line ends in relation to the first line.

Nah, They are identical, they aren't really called that, in our workflow we used to put the fonts in a folder outside of the document fonts (which for illustrative purposes I called old fonts), when cs6 came out and started autoloading fonts in the Document fonts folder that is next to the indesign document, we changed our master folders to put the fonts there saving us the step of using suitcase to load the fonts.  Both folders are absolutely identical though.

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