Use Ctrl+Q to rebuild before publishing.
One possible cause is SOLIDWORKS intelligently flip text direction as you rotate the model for easier reading, but Adobe Reader doesn't have that auto-flipping capability. So before capturing a 3D view or publishing to 3D PDF, please activate the corresponding annotation view. Make sure you don't rotate the model too much to trigger the auto-text-flipping. This way, the captured 3D Views will be better prediction of 3D PDF results.