Hi Sanjeev,
There are several threads in which they have discussed the same problem regarding the cost centre issue where it gets updated in O.M but the same is not getting reflected in P.A.
But i clearly understand that once you updated in O.M manually it will reflect in P.A but in case of LSMW it will not and for this there is a work around where you have update manually cost centres against PERNR,
Please check the below link,
http://scn.sap.com/thread/1157119
Hope this solves your issue and do mark if the above answer is helpful or correct.
Regards,
Mithun K