The only reason disabling the “updatenotification” module helps is because it is set to a location of “top_bar”, removing it allows everything to move over. I tracked this down to the CSS of course. He basically removed all region stuff and put in only two grid tags. The problem is that there is a div for “top_bar” (not to be confused with the location top_bar), then a container in that, with top_left, top_middle, and top_right within that. The container tag is for the top_bar. Since there is only one CSS tag for each of the top and bottom bars, nothing says to do anything special with the top_bar location so the top_bar is not separate from the top left middle and right. When a grid is used, everything just populates the grid, the top_bar is not separated from the top left, middle and right. This sort of confusing since the top_bar div contains “container”, “top_left”, “top_middle”, and “top_right”. I should say it confuses me, probably doesn’t confuse anyone who knows what they are doing. It’s just that if you style top_bar, it affects “top_bar”, “top_right”, “top_middle”, and “top_left”. It appears you need to style the container.
Again, just an observation looking at it in dev view, I don’t really know how it works. I was able to get it to work by using a “grid-area” for the container and setting it to span one row and 3 columns for the top and bottom containers. I don’t know if this really will break if other modules are added to other locations or more than one module is added to a particular location.