Hi Anant,
Go to the BAPI's source code and put an external breakpoint using the button on top with a 'Stop' mark on it.
When you execute the JCO function from MII, the execution will come and stop in your BAPI at the breakpoint taht you have set.
This is how you can compare JCO and JRA. Analyze the difference between the execution when flow stops on using JCO vs the flow while using JRA from MII side.
Thanks,
Rutika