I've been wrestling with this problem on my individual entry archive pages where the side bar falls down to the bottom of the page instead of staying on the right, and I just can't seem to figure out what's making it do that. On some entries the side bar shows up where it's supposed to, but on most of the entry pages it shows up at the bottom.
Individual entry pages are the only place it does that too. I've tried making the size of the #container and #beta divs larger to no avail. I have a feeling it could be some of the content in the sidebar that's doing it, but I don't know why it doesn't happen on all the individual entry pages if that's the case.