A dopey question, but does the system have to be restarted after installing APE?
The installer doesn't say anything about it, and the APE Manager shows up in System Preferences immediately, so it seems like a restart/logout isn't necessary.
But... I installed the ClearDock module, and after I click "apply" the dock restarts, but the settings don't take effect.
My computer's in the middle of some tasks right now, so I'd rather not restart if the problem lies somewhere else.