Hi, welcome to the forums,
Perhaps someone can explain it better than I can, but by opening things in the same window you're going to make it difficult to get back to where you were in the module (if that's what you want to happen). The original module isn't running in the background somewhere for you to go back to, as far as I'm aware. So while that probably works okay for your menu system, I'm confused as to how it's supposed to work for the simulations.
May I ask why you're linking to outside simulation SWFs, instead of just copying/pasting those sildes into the five modules? It seems like an overly complicated way to do things, at least from how you've described it.