I used a different templat on another site i have www.betterbuynow.com and did not have the same issue.
Yes, that's because some of the templates are fluid but Sophy Blue is not fluid it's fixed width.

Try to align the column and sideboxes with the same configuration settings given in the template readme file. If that doesn't work then you will have to play a little with the numbers until you align them.

Then you will have to recreate the header to whatever width you want it.