Scratch

There seem to be some important differences between the offline and the online-Scratch Running Enviroment (as I understand it, offline is based on Squeak Smaltalk and online on a Java VM). My children and me made a complex Scratch game, that works pretty good offline, but causes problems online:
http://scratch.mit.edu/projects/vally/1224
Main problem are invisible sprites that react in the Java-Enviroment like they were visible, but there seem to be also some other differences (e.g. Key-Buffering and visible parts of background pictures). One reason could be, that we did multiple web-uploads, to update the game (sometime we had a mix of pictures of the old and new version of our game, that vanished after we recreated the pictures as new items).
Could you help us?