smu1215, unfortunately the true Fullscreen mode is likely to not work properly or cause bugs, although it's less buggy than the built-in level transitions from what I've seen.
In the case of fullscreen, you might be able to set window size dynamically (not tried this yet), and for level transitions only use events and sprites/etc.
Edit: Here's a forum post with some helpful notes on fullscreen
http://www.scirra.com/forum/topic63779.html