Hussar
Legend
I'm not entirely convinced that they knew. There are enough CRs that seem so totally out of whack, that it looks to me like they were eyeballing it.
Yeah, well, there is that. And I believe that the designers have talked about that in the past. The CR's were a lot of eyeballing and, with so many monsters, I can see mistakes being made. Hello Mr. Ogre -

But, that still doesn't mean that they couldn't have done some analysis after the fact. Maybe in the DMG 2 or a web goodie. CR is a great idea and a serious boon to DM's (IMO). It just needs some polishing.