So I was having some issues applying a boolean to a cylinder in another project, and after troubleshooting and come to no solution I decided to see if I could get it to work on a blank project with the cube that spawns in when you open a new project. It still wont apply the boolean modifier. I did try removing doubles and recalculating normals.
EDIT: This is the project I am having trouble with. I am trying to use a cylinder to cut a headphone jack hole in the bottom.