I've not had this issue before, but since upgrading XCode and Cocos2D. I noticed this when creating a blank Box2D Project. Can't embed a screenshot, so I'll best explain.
The world box is at bottom left but only a portion showing and the A B C D images are being displayed as one sprite ie:
and not individual as I would expect. Also the DEBUG Draw box is not around the sprite where I would expect it, it's below by about 100 pixels. Wish I could attach a screen shot to help, but I can't sorry.
Like I said I just created a blank Box2d project, and ran it to see the boxes when I tapped the screen.. by the way the Tap Screen message is top centre as expected. I've tried running in Retina and non-retina. Same issue for both runs expect the sprites are drawing as expected from the sprite sheet as individual A B C D sprite and not just one sheet with all four as per above.
Hope this helps??