The term "pop up" might not have been used in the traditional sense, but your right, typically those block your view when opened, or you hover over a word that hyperlinked and up comes something else.

In this instant case, the ads are huge on typically on the right side of the screen. They make a page where you can post/read a comment go from 13 inches across down to 6 inches. There are a couple of examples already posted in this thread. It's the same regardless of IE, Mozilla, or phone/tablet usage.

If it's an intentional change, it is what it is. The site has the right to monetize the pages as they see fit, it's just cumbersome and not user friendly.