Hi Rohit,
Put a breakpoint in FM COM_BUPA_MAIN_INBOUND_ISU in ECC system. Inside this FM it first create customer using FM PI_BP_PROXY_BAPI_CUSTOMER at line 187.
IS_CUSTOMER flag you can find in b-doc structure LS_BP_EXTERN-CRM_DATA-SALESCLASS-DATA-IS_CUSTOME.
Before calling FM PI_BP_PROXY_BAPI_CUSTOMER system perfroms multiple checks if they all went succesfull then you have to debug inside FM PI_BP_PROXY_BAPI_CUSTOMER for finding out the root cause.
Thanks,
Ashish