I have been testing the 1.0a code in this excellent plugin and have found a problem. There is a typo.
The variable $shiwafter is referenced in the first line of code (line 21 I think, a function), when it should be $showafter.
The effect of the typo is to not insert a </div> tag and so cause the remaining elements in the page to stay within the formatting influence of #content. All of the left and right side bar elements then line up below all the contentin the centre column. I hope this is helpful.