The section bubbles are just multi-view blocks that themselves host a regular block. You can add the StandardSectionBubble multi-view block to your template and modify the block to how you want it. It will then always be the way that you want.
If you want to permantly change it so that you don't have to keep it in your template then I believe that you can change the block in the following file.
C:\ProgramData\Autodesk\MEP 2014\enu\Styles\Imperial\SectionStyles.dwg
If you are using metric or global then you will need to modify the directory string and change Imperial to either metric or global. I would recommend backing up the original file if you go this route to make sure that you can revert to the original if your changes have unintended consequences.
Hope this helps.
P.S. the block is annotative so if your drawing is set to 1:1 then that could be your problem.