Hm...
One possibility to get around the playbar applying to the entire module would be to create another set of custom navigation buttons and use those on the simulation slides instead. You can create a play/pause button, a button that skips forward a certain number of frames and a button that skips backward a certain number of frames (to mimic the fast forward and rewind buttons), and a button that skips back to the first slide of the simulation (like a rewind button).
Another possibility is to split the modules up further. Say a module has 4 slides, then a simulation, then 2 slides, then a simulation, etc. You could link from the menu to a swf with the first 4 slides, then link to a simulation, then link to the swf with the next two slides, then link to the next simulation. (So 4 swfs in total, instead of 1 main module and 2 simulations.) The downside is that I'm not sure how you could implement backwards navigation between swfs...
(I'm sure I've seen something about linking to a specific slide in a course, but that was a long time ago... That would help you go from a main module, to a simulation, and then back to the next slide in the main module, without doing either of my suggestions above.)
I'm not very familiar with packaging an entire course with modules into an .exe, since most of the courses I make go into an LMS with its own menu system. Maybe someone out there has done this before and can share their methods. *fingers crossed* Image may be NSFW.
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