A few things to try:

1. In your game options deselect the "Use mods" option if it is selected/highlighted.

If that doesn't work:

2. Rename your "../My Documents/My Games/Fallen Enchantress/" directory to "../My Documents/My Games/Fallen Enchantress.old/"

Please let us know if either of those effects your issue.

Patch for me and missing trees. Ran in admin mode, trees back. Same thing I experienced in previous builds.

1. Deselecting "use mods" had no effect.

2. Renaming - When I recreated my custom Sov & Race, saved a game, exited to main menu, and tried to start new game the graphics were ok.

Just acknowledging the missing tree issue.  Can see them on the cloth map, but zoomed in they're not there (I thought such an expansive plain was odd).

Derek - I don't think it had anything to do with an old Sov.  There were no pre-existing files in Units or Race folders after the update.   I created him new both times.

 As a matter of fact after playing the game for about an hour the graphics glitch was back.

Here are the files from the new version.

https://www.dropbox.com/s/u2emfndhtmblw0v/Faction_Jedi.xml

https://www.dropbox.com/s/smw8r520gfoeulo/Lord%20Vader_1472866095-5404.xml

https://www.dropbox.com/s/4k9cu2xr58qe8lo/99_1_4.EleSav 

Here are the files from FE.old.

https://www.dropbox.com/s/0eirav6csihd76s/Lord%20Vader_1879150029-469.xml

https://www.dropbox.com/s/526mz5rak5om6rd/Faction_Jedi_old.xml

https://www.dropbox.com/s/q12w2x8f289536p/Jim_99_1_4.EleSav

I can do a clean install tomorrow & see if it happens again.

Did a clean install and graphics issue has not returned.  Played about 1 hour and tried to start new game several times from inside current game.

Looks like it was linked to the patch update & old files not working.

I'm also getting many missing graphics issues, though instead of UI my champions are missing heads and trees/structures disappear unless I zoom in and out a lot.