Whenever I upload my game, the timing gets messed up. The actual game goes off during the mini-movie. Everything is fine when I look at it in the application on my computer! What's going on?
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The online viewer is programmed in a different language than the Scratch program; therefore, projects won't run exactly the same online than they do offline.
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There's more about this issue in the FAQ section in this topic
http://scratch.mit.edu/forums/viewtopic.php?id=15657
maybe you will find some pointers that will help you out.
The good news is that when Scratch 2.0 is finally rolled out completely (and I don't know when that will be exactly), this problem should go away since the place you build the projects will be online too and there will only be one program that displays projects instead of the two we have now.
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