This behavior has been observed with Agent for IBM WebSphere Application Server 6.0. Though rare, CLASPATH variable settings can be cleared after the agentadmin command is executed.
Workaround: Manually add the following entries to the CLASPATH variable of the IBM WebSphere Application Server 6.0 instance (where agent_001 is an example of the agent instance. It might be another instance, such as a agent_002or agent_003):
PolicyAgent-base/agent_00x/config
PolicyAgent-base/locale