When opening a molecule as a .FChk file, the atoms no longer render as sphere in ball and stick mode, instead they're roughly icosahedral polyhedra. I've used this software to make publication quality orbital renderings in the past. I've attempted uninstalling and reinstalling without change.
Cheers,
Nick
You clearly have set the atoms to render as Polygon - if you uncheck that option and use "Ball and Stick" it will look fine.