Dear Chethan,
As per your explanation system behaving correctly. I Am not saying that i don't want /3I9 when contribution made through IT 587.
User in a prejudice view that /3I9 Sec 80CCD(1B) should not generate through salary, i.e IT 0587. Even though i have explained them by different examples including your explanation/views in this post, they are reluctant to listen and not convincing.
I have already attached their mail that represents "National Pension Fund does not exceed to 150000 only under sec 80ccd(1) and the amount over and above is not carried to 80CCD(1B) ".
Regards,
Mastan