The problem is that FL was made by Microsoft with little thought to the future of it - and plenty of not-logical things going on ingame. I don't personally know what the scripting is like inside the FL files, but I'm making an assumption here (pretty safe to assume I think) that because it was made by Microsoft...
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Actually, FL was first made by Digital Anvil, an independant software company that had big, big plans for the game (everything that was originally promised) but was then bought out by Microsoft, who then took over completion of the game. This had the result of mixing two different programming styles, which in my programming experience generally results in code that resembles scrambled eggs.
Scrambled eggs code is very difficult to deal with.