If you see here: http://admincentral.org/
You will notice that between the forum icons on the left and the latest post box on the right there is no gap between them and the border.
I had removed the padding so the category strip could look the way it does but no my XenForo test board on my local server I did this on the default theme and it worked perfectly like that with padding on both sides.
I can't see anything that could be affecting this within the themes .xml file.
If anyone had any idea that would be great.