Sankar,
Why dont you try this on a completely new role and see how this works.
Did you use expert mode with third option to generate your role. If you still see objects there which are not supposed to be in as per proposal values in SU24, it can be the case that those objects have manual or changed status. Also ensure there are no other tcodes in the menu which also uses same objects.
Coming to your original query, S_TCODE is always updated when ever you add a tcode into the menu without any exceptions.
Good luck in investigating further.
Thanks,
Brahmeshwar