Hi Manas,
For this scenerio, there should be two system objects in Portal Landscape.
a. The one that connects to ECC. i.e. the WebAs and ITS URL's point to ABAP system... the alias is generally SAP_ECC and other alias are added to this as well like human resource
b. Webdynpro Launch System: Exactly the same as a. But the ITS and WebAs URL should have portal server URL... the sole purpose of this system object is to launch webdynpro java applications from UWL workitems. Maintain alias SAP_XSS_WEBDYNPRO.
Now configure your UWL in UWL Admin. There when you define a connector , enter SAP_XSS_WEBDYNPRO in the webdynpro launch system.
Also maintain correct properties in SWFVISU transaction in ECC.
Release UWL cache and re-register.
Logoff and log back in. the issue should be solved after this.
Ankur