Quote: "Include file added via the IDE get appended at the end of the main source. #Included files get added at the point of inclusion by the compiler."
Have you verified that with a source code example? I thought that too but IanM debunked my assumption and said #include just appends to the end of the main source. I didn't try it out to confirm because I never use #include anyway, but I assume IanM was right because he always is.
@MikeK
As mentioned before you should setup a gosub routine to declare global variables, etc. and just call it from your main source. Nothing wrong with doing that, in my opinion, and it's actually neater than assuming execution should run all the way through a #include file.
Something tells me you're not using functions at all in these included files?

A 3D marble platformer using Newton physics.