Thanks for the reply Ivan and sorry for not responding any sooner. I looked in to these notes and could see that we have all the parameters with the right values. I'm currently looking to add the Portal URLs to the white list of the Popup blocker and see if that helps in closing the connections on the ABAP side. One of the notes suggested trying this. I will keep you posted.
Regarding my second question, I still can't figure out which particular RFC Destination or Jco RFC Provider is used to connect from Portal to BW. We currently have only one Jco RFC Provider and I turned it off and tried using the portal. It was still able to connect to BW and run the reports. So I'm not sure how it is connecting to BW ABAP.
Thanks