When a WebSphere server instance that is created in one machine is federated into the deployment manager of another machine that already has server instances with J2EE Agent installed, the newly federated server instance will not start. This is because, the security configuration changes that are performed applies to all the instances of the deployment manager and all the application server instances that are part of it.
To work around this problem, copy the following files from the $WAS_HOME$/lib folder of the machine that has agents installed, to the $WAS_HOME$/lib folder of the new machine, then restart the server:
NidsCommonAgent-unsign.jar
NidsWebSphere-unsign.jar
nxpe.jar
jcc-unsign.jar
nxpe-toolkit-unsign.jar