I fired off my SSHAgentServices plugin to Rick since he's as much of an ssh nut as I am. He noticed something I hadn't... apps launched by the Finder didnt' get the environment variables. I guess I'm enough of a Dock and Terminal weenie that I never use the Finder and didn't catch that one. Anyway, I noted the restriction in my readme and started trying to figure out how to get around it.
I found QA1067 which indicated the Finder would pass along environment variables. So what happened?
Found it. The Finder is launched before the plugins are run, the Dock afterward. That explains why the Dock gets the variables and the Finder doesn't.