11.04 Natty Narwhal - minimized windows disappear, app still running

I'm thinking this is due to some file corruption on disk. Basically, my 11.04 installation has worked great until recently.
Now, when I minimize a window, it simply disappears, even though System Monitor shows it still running (sleeping).

Before this problem occurred a minimized window could be restored or maximized from its respective workspace, just as you might expect it to do.

I have the workspace switcher, so my work around has been to open each window in a separate workspace. But it's annoying and
sometimes I forget and open a new app in the same workspace and BAM the previous application window disappears as described above.

What's to be done? Is there some part of 11.04 I could re-install? A window manager or something? I know just enough about linux to be dangerous, so if you have a solution PLEASE DESCRIBE IT IN EXCRUCIATING DETAIL