Comment 6 for bug 368156

This isn't exactly related to compositing being unavailable. In that case, Do will default back to showing the Classic non-composite theme. The moment compositing shows up it would then switch back to Docky theme.

There is a race condition where something tries to update the dock window before it is displayed, and GTK goes nuts and winds up making the dock window invisible.

I'm still tracking down what causes this, but the good news is restarting usually fixes it right up.