This bug really drives me nuts.
When I ran across this bug (
http://community.stencyl.com/index.php/topic,8363.msg52337.html#msg52337 ) when adding a new button while the Scene Editor was open, I added multiple instances of a same thing and when I tried it AFTER I saved it and reopened it again, I decided to clean up the mess. After doing that I closed the Scene Editor with saving, I saw that the thumbnail changed and when I tested it the level changed too, but when I open the scene editor again, it was the same mess as before. I closed it without doing anything and closed Stencyl with saving. Restarted it, and it changed.

Issue:
1) Stencyl opened the scene editor with data from the last time I saved, which has been edited and saved after that, but the changes did not apply to the opened scene.
2) The bug as described in this post (
http://community.stencyl.com/index.php/topic,8363.msg52337.html#msg52337 )
Os: Ubuntu 12.04 Precise
Stencyl version: 2.0.0 b500
Log attached