Why does the tracking I set in eDocBuilder not match what Illustrator says the text's tracking is?

There is a difference is how tracking is measured in eDocBuilder vs. Illustrator. eDocBuilder uses the word "tracking" as it was more commonly defined several years ago-- 1/200 of an em. The eDocBuilder code converts that tracking value to a value usable for the CharSpacing attribute in PDFs.
Adobe Illustrator uses a different definition of tracking than eDocBuilder. Illustrator measures tracking in 1/1000 of an em, so it takes a higher number in Illustrator to achieve the equivalent tracking in Illustrator than you would achieve in eDocBuilder.
We are unfortunately not able to change eDocBuilder's definition of tracking to match that used in Illustrator. There are too many templates in use and too many users who are accustomed to eDocBuilder's current tracking method for this to be a smooth change.