In Chrome 53 popup alerts aren't showing up.
I've tested with versions through 48 to 53 (gotten from here) and concluded that it was Chrome 53 has this problem.
I've also tested with fresh profile.
Chrome 53 comes with Material Design UI which I thought was causing it but disabling it didn't help.
Here's a video. In the console tab I type a simple alert('hi') and hit enter and it doesn't shows up. It's there but not visible because it takes away the control and I can't type anymore in the console tab. I keep clicking around (not shown in the video) and finally I manage to tell the (invisible) popup to go away by hitting Escape at which point I can type again:

Anyone else experiencing this?
PS: Same with the Profile popup that comes from the button on the top right.