Rishi,
I see that the indicator is not tick for ShpNt in Checking Group. Is this the reason ?
Yes.
Why does the PP checking rule not take in to effect, the possible Receipts like ShpNt/Prod ord / Pld ords etc.
Because you have not configured it to do so. These settings commonly differ from system to system, and from company to company. They can be changed via OPJJ.
...It does not give a true picture of Missing part situation.
Well, that is an opinion, which evidently was not shared by the person who created these settings in your system; or else he was not even concerned about such matters.
There are no 'right' or 'wrong' settings for OPJJ. The only concept is that they should meet business requirements. I suggest you find out why these settings were chosen IN YOUR SYSTEM before you elect to change them.
Best Regards,
DB49