The System agent does not source /etc/auto.profile
Set the following in agentparm.txt and restart the Agent:
oscomponent.profiles.global.override=true
When this one is set, the following will be true:
oscomponent.environment.variable_manager_$AUTOSERV_SCH=/opt/CA/WorkloadAutomationAE/SystemAgent/WA_AGENT/profiles/$AUTOSERV.txt
Note: The value of $AUTOSERV is your 3 character AutoSys instance name.
In /opt/CA/WorkloadAutomationAE/SystemAgent/WA_AGENT/profiles/$AUTOSERV.txt set:
EWAGLOBALPROFILE=/etc/auto.profile