There can be many reasons why sidebars end up at the bottom of a site. On my site I found the stats counter was the culprit. We’ve also found posts that creeped into the sidebars distorting things – and then validation is important, the smallest things can screw everything up.
Make sure you dissect your sidebar and put things back one at a time, you can find wayward code that way as well.
By the way, after spending hours reading the docs and support posts here – what a bunch of angst-ridden moderators troll this place. Insults, backhanded advice, petty condescension and flippant comments are the norm. If you guys are unhappy, do us all a favor – shut the computer off and drink yourself to sleep. I must have read 50 posts where Moshu or Whooami just tee off on people – WTF? When I started using WordPress I made some stupid mistakes, but it was no fun coming in here to learn from them – too much insecurity here. People who get their thrills cutting down newbies are a sorry bunch…