Thank you
The issue got fixed after we changed the system ID value to UPPER CAS in CMC->AUTHENTICATION->SAP->OPTIONS TAB->SYSTEM ID.
We entered our BOBJ Server in System ID, but in lower case, because that is the name of the BOBJ server/node.
But the System ID that the STRUSTSSO2 in BW creates is Upper Case (even though we provided is lower case). But when we rechecked we found that the System ID it created is Upper Case.
So we came back and changed the System ID in BOBJ CMC and it all worked, So I guess it is case sensitive.
Thanks anyways :-)