Ok. Sometimes (not always in this case) when you go to edit the themes WordPress deletes some formatting just as you submit the new code.
I’ve had issues with this before in the create page area where WordPress likes to get rid of seemingly un-needed formatting and it ruins the page. Even if you just switch between “Visual” and “Code” it eats away at the code until there’s no formatting left.
It’s strange that it would cause Flash not to be able to change the page though.
Temporary fix for anyone who stumbles upon the same problem:
Reinsert the Flash code and if necessary give it some extra spacing to eat at. That’s what I did and it works fine now.
Still, if anyone has a better solution please post it. I feel that the problem will probably return.