I was installing and uninstalling components last night and I managed to really screw something up really bad.. Fedora still operates but, not very well..

I think everything went fubar when I installed the SMART package manager. I've also been having issues with my graphics drivers so, that may be a cause aswell.

So this is what's happening. When I first start x and log in, there are two ghost "untitled" windows at the task bar that do nothing. They just sit there. You can't maximise them, delete them, they don't do anything. Also, when I load a program like firefox, it does NOT appear in the task bar, only those two untitled windows are there.
An other thing is, when I load a program, I don't have the options to close, minimize or maximize the window. The options just aren't there. And the window is stuck in the top left hand side of the screen. It's almost as if part of my gui is missing or something..

Help!!

Have you tried creating a new user to see if the problem is system-wide, or if it just affects your user? If that is the case, then the easiest way to fix it is probably to remove the Gnome configuration files from your home directory. http://www.yolinux.com/TUTORIALS/GNOME.html that link has a table entitled "GNOME user configuration files and directories" with all the gnome configuration directories. If you move those to a temporary directory in your home directory, log out, and then log in again, all should be back to the default values. You'll have lost any customisations you made, but they should be relatively straight forward to redo.