How to change properties of holes?
As i mentioned in the comments the Gerber files generated and displayed with no problem. There must be a problem with the way you are generating them. Watch this video.
http://eapbg.com/2015/08/13/eapbg-2-impromptu-eagle-board-layout/
At the very end of the video I go over how to generate Gerber files. Also there is a link to the job file i used.