OS X :: Applications In Dock Suddenly Missing - Little Ball Showing Open

I have an iBookG4 with Leopard. This morning I may have had too many applications going at once--camera applications plus listening to a talk using RealPlayer. Suddenly everything froze, but I got it all going again. However, now the little balls that appear under an application icon to show that the app. is open are missing. Also, when I click the icon, e.g., for Firefox which I'm using right now, the pop-up menu gives me the option to "Open" it, when, obviously, it's already open. There is no "Close" option in the menu anymore. I AM able to quit applications by clicking their name in the menu bar at the top of the screen. But I'm disturbed that this weirdness has happened. Things I've tried already, without effect:

1. Restarted computer. The computer won't shut down. Everything on my desktop disappears except for the wallpaper and the Dock.

2. Shut down computer (chose "Shut Down" as opposed to "Restart"). Same as #1. Won't shut down.

3. "Force Quit"--clicking on the Apple icon > Force Quit > clicking on the name of the application in the little window. Note: I haven't used Word this morning, but Apple icon > Force Quit > [little window] brought up a whole list of applications I haven't used, inc. Word.

4. Repair Disc Permissions