I had a look at your example and the issue appears to be related to the auto column span. Regardless of if the sub regions have content and styling set the autosize functionality is not functioning correctly. I'm not sure if this is suitable for you but I removed the styling from sub reason 1 and instead set a column span of 3 on both sub a and sub b. By using a set column span this appears to resolve the issue.
Hope this helps.
I'm still getting used to the grid layout and visualising what's going on. I saw a great presentation recently by mark.lancaster that helped explain the RWD layout.
Would be nifty if APEX embedded some of the debugging tools I saw.