Using JES 5 b12 on Windows, if Application Server is selected at the top level of the select components installation panel, then the Node Agent subcomponent is also selected by default. The installation process subsequently creates a node agent and a server instance named AppServer1 that belongs to this node agent. This is the correct behavior.
However, if the Node Agent subcomponent is deselected, the installation process still creates an AppServer1 instance in the common.properties file for the domain; for example:
Subsequent attempts to deploy applications using asant will fail.
Edit the common.propeties file, replacing appserver.instance=AppServer1 with appserver.instance=server.