Just some of the more popular ones.  Weapons mod, expanded factions, and adventure pack.  All of which I already got rid of on last install, including both other awkward locations that elemental chooses to store things.  Upon reinstall it still has the old improvements lit.

tried that too.  I didn't keep any saves.  I didn't keep anything.  I completely removed all the files in all 3 locations stickied in this forum.  Mods are disabled by default on installation (because I deleted the entire files, thus prefs was gone)

Maybe i misunderstood you, but I deleted the data.zip file in the data directory of my \games\elemental war of magic directory and had it rezip it upon running with no discernible difference compared to before.  Same symptoms.  Deleting any other other folder structures from my install directory seems to result in the game not loading up properly.  Like the words don't load up on the menus, or it just crashes on startup.  So I restored those files, and I seem to be right back where i started.

Ok,done.  No change other than it required a good 5 to 10 minutes to get past the splash screen. (I know, datazip remaking the data.zip file, stardock should really give you a visual indication that something is happening)  But upon starting a new game, I still have the same old global mana but no population based economy buildings.

Fixed it!  For any future people having this problem:

The folder structure for improvements is as follows:

Data> English > Core Improvements

Inside this folder there are 8 improvements files that also appear inside a further subfolder called Only-SP (only single player maybe).  When the game updated, it changed the files in Core Improvements, but not the ones in Only-SP.  I copied the 8 .xml files over into the only-sp folder and I now have the proper improvements list.  The files are all of the Kingdom_______Improvements and Empire_______Improvements.