The Agent runs as root user. When this is the case, the JOB with USER specified processed by the Agent, ULIMIT for the USER is not used.
The WA Agent may be started as root. The agent then runs the jobs as user from the job. The spawned process will inherit the limits of the root or user that started the agent.
Set the ulimit of root or user that starts the agent to a higher limit.
Alternatively, set the ulimit in scripts that are being executed by the agent.