The reason for "screwy behavior" is not due to Dock-A-Bye missbehaving, it is due to the Dock quiting. Dock-A-Bye is a perfectly safe application, although I make no guarantees about its ability to successfully kill the dock. It quits totally after the Dock has quit totally. (Unfortunately on some of the newer systems, Dock-A-Bye isn't fast enough to quit the Dock before the Dock restarts itself again, and after about 20 seconds Dock-A-Bye admits defeat and quits.) Unlike popular belief, Dock-A-Bye is NOT still running.

TECHNICAL REASON: The Dock provides other services such as the desktop picture, minimization of windows, and apple-tab application switcher, as of OX X 10.2. Therefore when the Dock is quit, those services are quit too! (This reason, among others, is why it is unsupported in OS X 10.2, meaning that I know what it does and I can't fix Apple's code. I am not using Dock-A-Bye anymore.)

Dock-A-Bye tries repetativly to quit the dock until the Dock has stopped restarting itself. While this is happening the dock will quit/restart/quit/restart/... and the desktop picture will correspondingly dissappear/change/dissapear/change/... which produces that flickering effect if Desktop Settings are set to "change picture every xxx". Once the Dock has stopped restarting itself (or once Dock-A-Bye has timed-out and quit), all flickering behavior ceases.