When I decided to go for sidebar menu, I knew it will cause issue with any site using portal. But on the other hand, its made for core SMF and it does well with it. However, at once I thought I should give option to disable side menu but then sidemenu is the main hightlight of this theme.. can't do that !
Also, I am glad Ozzie that you liked my theme, its just unfortunate that the layout I decided for this theme is not suitable for for forums using Portals. However, as Runic said, its not that hard to manage but not straight forward either.