Hi Dinesh
You have the answer for your question!
"In BW system, we use a Standard DSO as a target with key fields “PO Doc Number, PO Item and Process Key”"
The above point gives the reason for the problem.
The way you change the plant before GR is something different, I hope. Standard DSOs will not work as per our expectation. They are created for their own purpose. You could try using the cube 0PUR_C01 which is also standard and could load directly from the mentioned datasource. This might also help.
Else create a new DSO with Plant, material etc as well in key field, that should do the magic for you.
Hope this helps
Regards
Karthik