I had the exact same problem, but I think I managed to fix it.
I went into Prefs.ini in My Documents\My Games\Elemental and changed RegenerateTextureAtlas to 1. (I also tried choosing a couple different values for the max atlas values, but I think this is the change that fixed it.)
After running the game with that set to 1, the UI appears normal, and I am able to change graphics settings (including the texture atlas setting) without it disappearing again.
Elemental 0.805
2x GeForce 8800 GTS (with SLI), drivers are 257.21
Windows 7 64-bit / DirectX 11