At a minimum, perhaps that means USIEF (the corresponding agency in India) has started looking at our applications? I think it is probably neutral if you included scanned versions via interfolio with your initial application.
In the e-mail we received when we were notified of being recommended, there is a link to a website http://us.fulbrightonline.org/information-for-recommended-candidatesthat says that failure to submit your official transcripts could delay your final notification. So, I don't think it will have any bearing on their actual decision? Best of luck, I'm applying to India for research too!