Hi
Take the help of any ABAPer and use rsa3 extraction through ABAP debugger. Put some breakpoint in the code. You would be able to understand whether the records are being extracted or not and if yes then where are they getting removed. This will help you surely to pin point the issue. Many a times when issue like these come, we debug through rsa3 and we get the list of data being processed and if we find some data missing then we are able to find the point of the code.
Hope this helps.
Mohamed Shadab