unfortunately, your question is in regards to your personal implementation of some equations in Matlab and not a quesiton on how to use MathWorks products. It is not likely someone will debug your matlab file to find out why it isn't working unless you identify a specific bug/problem that you need help with.
Some generic advice about creating your own models. You could consider using a higher order solver, but if time step has no effect, it is likely that either your model is implemented wrong, or the equations you are using are not appropriate and different model equations should be used. You can use ctrl+u to look specifically at how the equations are implemented in Simulink and use this to better consider your matlab implementation.