It may be that you've made either the content area or the sidebar wide enough that they can't occupy the same horizontal space on the page ... and so your browser leaves the content area (which comes first in the template) in the correct area, but bumps the sidebar below that.
The solution, presuming this is the issue, would be to check your width specifications ... including anything you put into the content area, the sidebar, etc.
Ah ... it's also possible that your coding is incorrect (for instance, you closed a <div> before you should have), and so I'd also check your code. The W3.org code validators are great for that purpose:
Sadly, the validator won't add up your widths and tell you if there's an error. <grin>