Hi Raja,
Yes, BW Java UME is BW ABAP.
We have BW ABAP certificate imported into BW Java and SSO works between them.
I think when external facing portal presents the MYSAPSSO2 logon ticket to BW Java, BW Java is not looking up usermapping user id. I'm not sure if this is known limitation with Java to Java SSO with different user ids !
Regards
Siva