I have a single weblogic server instance that displays incorrectly as being down. The rest of the instances on the same middleware domain display correctly. I've reinstalled the client agent, but that has not resolved the issue.
There are several possibilities, but first it will help to understand how you are configured in regards to your agent deployment and setup. I assume your WLS instances are in a single domain in this case spread across multiple hosts. Do you have individual EM agents on each of the host machines? What version of WLS are you using? Also, is this EM 12c PS1? It likely is, but did want to confirm.