Is there any difference between GUI s-function solver & matlab m-file solver?

I think the answer(result) of those simulations should be equal.

1.GUI s-function > sim('mdl') code

 in GUI s-function
  sim('mymodel');  % mymodel.mdl

2.GUI s-function > m-file > sim('mdl) code

 in GUI s-function
  start;  % start.m

 in start.m-file
  sim('mymodel');

But it isn't...

Is there any problem or difference between those ways?