launching the application through equinox launcher vs through eclipse.ini

This in-tune with my SOF post increasing the stack size while launching RCP application

I could able to launch the RCP based application by a cmd file ( windows batch script) but the same I am trying to do over a ini file but not working.
Just wonted to understand what is the difference between these two approaches or if I can setup a debug run to understand what causes the launcher to have stack overflow error during launching.
Any pointer would be highly appreciated.