Hi, I'm still on 3.3.3. and I'm experiencing the same problem as I had long ago on another 3 column theme.
Some of the plugins, like Social News Nederland and the famous Yet Another Related Posts Plugin (YARPP) display their results or icons at the bottom of every article.
Irritating enough they also show up in an ugly way on the right sidebar!
Again, Atahualpa doesn't seem to be the only one with this problem, so it might be plugin related. Still, I'm looking for the code to change to stop it showing up.
I'll give you an example: http://salek.nl/blog/2009/06/geld-ui...-goede-doelen/
You will find 3 related articles at the end of the article. Somehow the also show up on the right sidebar while no one put it there!
Any suggestions other then disabling those plugins?