I can see two options here:
1. Something in your system prevents dynamiclinkmanager from normal communication while AE is not running;
2. Adobe Dynamic Link improvements for CS6 resulted in utilising advantages of multiple processes while AE is running.
Guess, Todd could shed some light if the latter has something to do with reality.
From practical angle relying on Dynamic Link in a project where complex AE compositions are involded is not wise.
See this thread on Dynamic Link workflow, pay attention to Todd's comments.