This is not a permanent solution but what I did as a work around (which will break on the next update) is to change the home.php as follows:
if ( ! is_active_sidebar( 'blog' ) ) $col_width = 'span12';
if ( ! is_active_sidebar( 'blog' ) ) $col_width = 'span9';
The problem is the template doesn't seem to know that the blog sidebar is active. Put you widgets in the blog side bar and this should work.
NOTE: This is specific to the home.php file for the home page. If you are having similar issues with other pages, look at page.php for similar issue. span12 = width 100% so there is no room for the sidebar. You probably didn't notice it but the sidebar gets wrapped underneath the blogs. Hope this helps.