I also noticed that any attempt to force my LaunchAgent to start from terminal (via SSH session) seems to be ignored. The LaunchAgent still does not start running until all the Applications have been restored. For example, the follow has no effect:
launchctl load -w /Library/LaunchAgents/com.mycompany.myproduct.myagent.plist
Topic:
App & System Services
SubTopic:
Core OS
Tags: