This is a bit hard to solve just like that without any details on the applications you have and what path you took to get to the second deployed application.
I have found though that the main reason for a section or item about the application being missing is that WebSphere does not recognize the application to have that capability. In the cases I have found this is because of deployment descriptor inconsistencies, for example:
- the deployment descriptors being in the wrong JEE version format
- One binding file referring to an ID of a item in another file, but that item actually has another ID (development tools can sometimes "help" you cause these inconsistencies.
I suggest you try to do a compare of the deployment descriptor files between the two deployed versions of the application.
If the application is exactly the same and you just changed these parameters at deployment, look for naming conflicts.