Either you're using the wrong EXE for the version of the game you have installed, or one of your mods has modified something it shouldn't really have modified. Make sure your game is fully updated via Steam, and then check that you've downloaded the most recent NoSteam EXE from the downloads page here.
The latest version of Litcube's Universe predates the latest patches of X3AP. Since LU modifies the .obj files, which don't include the changes from these patches, the version check fails leading to the displayed warning. The problem is known to the LU creators (see this post and the following reply by Litcube).