I have this problem with After Effects CS3 (8.0.1) on Leopard 10.5.1. I know that AE isn’t supposed to work with Leopard yet (not fully anyway), but I just thought I’d point this out. I usually hold down the option key and click on the desktop to minimize apps, but noticed that it doesn’t work with AE CS3. I also tried using the hide command from the apple menu but that doesn’t work either. Then I read this thread and tried the minimize button in the upper left corner of the window and that worked. Double clicking the title of the window also worked. However, when I click on the AE icon in the dock to maximize the window (unhide it), everything comes back except for the menu bar. I have to quit After Effects and relaunch it for it to work again. Hopefully the next AE CS3 patch will address this.