There are some limits in flash output, but none that should have this effect.
Do you see the same problem on DVD output?
You might post a screenshot of your flowchart.
I assume you are using overrides?
Do you have the end action of the scene menu set to the main menu? Is that really what you want? I don't see why your scene buttons don't work, but that strikes me as odd.
If that does not fix it, try removing the chapter end action on that last chapter. Yes, it should not matter, but something is odd.
Otherwise, I would try creating a simple version with one menu, linking to the movie. Confirm this works. Then one with two menus, with one for scenes (just a couple of chapters). Same problem?