The mesh files differ error is usually caused by the Trinity install. The easiest way to fix it is to go into the Sins of a Solar Empire install directory and deleting all the mesh files in the base, entrenchment and diplomacy Mesh directory and re-validating the installation through impulse.
you get the "Verify Installation" option in impulse by holding [ctrl]+[shift]+[right click] on the sins of a solar empire and expansion listings. This should re-install the meshes.
See here for a post from Stardock...
https://forums.sinsofasolarempire.com/368961