So digging into the XML files a bit more, it looks like the problem is messed up comments in the XML file (speaking specifically about KingdomSpecialImprovements.xml).  Maybe the engine is supposed to filter them out with some XSL or when they parse it... but that doesn't seem to be working for me when I run the game, so the net result is all the duplication.  The strange thing is that it worked fine before 1.06.  The really really strange thing is that the comments say version 1.123...  is it possible I have some file from a future patch somehow?

Delete your C:\Users\"Username"\Documents\My Games\Elemental folder, and afterwards open Impulse and shift+right click Elemental, click 'Verify Installation'.

Once Impulse is done checking and updating Elemental, check to see if the issue still persists after that.