Or install KDE for your Fedora and switch to using it. Personally (and it
is a matter of personal preference) I find KDE much easier to use and configure. (And the "Switch Session" option you get if you also change the display manager to KDM instead of GDM can be very handy at times.)
That -- that it's a "personal preference" matter -- said, you might find Mr. Tovaldis'
comments about GNOME interesting. (That link is only one of many returned by Google.)
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More to the point of your question, what were you doing when the stream of "pop-up" boxes was displayed? I've noticed that a similar behavior sometimes occurred when a script was incorrectly rendered by my browser. (You said that the system was idle for a few minutes, but what tasks were still running? A running system always has something running. Open a terminal window, run the
top command, and tell us what's shown as using resources when the pop-ups start to be displayed.)