This problem has to do with the way older versions of the HTML Editor handled mistakes in code. Versions 2009 and lower were more forgiving of mistakes in code, which, while easier in the short term, could create problems with your design down the road. HTML Editor 2010 SE creates more accurate code and cleans up any code that might be messed up. That cleanup process may explain why your website no longer looks like it used to.
To fix this problem, run the code cleaner by going to Tools > Code Cleaner. Alternately, you can use a service like HTML Tidy. Either of these options will clean up your code for you.