I found this interesting. One user asked how he can make the default navigation set to the right region when someone enables his theme. After experimentation and code digging, I found that drupal places the default blocks to the first region found IF

• drupal doesn't find any blocks for the theme
• the region assigned to it isn't supported by the theme

So in this case, the region must be defined as follows in the theme.info

regions[right] = Right bar
regions[content] = Content


If you have a left region and the old default theme blocks were assigned to the left region, then drupal assigns the blocks to your left region. You can't do anything about that.