I recently performed an upgrade from FC5 to FC6 using DVD, followed by a "yum update". My box runs KDE, not Gnome. After the upgrade with X and KDE running, most things seem to work about as they did before. However, each window seems to lose keyboard focus at random intervals. Sometimes between almost every keystroke, other times I can type a few paragraphs before the focus goes away.
When the focus is lost, the effect is that keystrokes don't seem to do anything. It is as though the program running in that window has hung or died, and at first I thought that was what was going on. However, I've discovered that simply moving the mouse cursor out of the window and then back in is enough to restore full keyboard function. My configuration is set to "focus follows mouse" so moving the cursor changes which window has focus.
There were a number of problems with the upgrade. (I mention them just in case they might have a bearing.) Updating with yum after the DVD upgrade was not pleasant. I was forced to remove about 100 packages before it would work, then add them back afterwards. It doesn't seem right that yum can catch a whole bunch of dependency problems that anaconda is happy to create. And strangely enough, the "yum update" did /not/ update yum itself, though it needed to be updated.
After the update, I ran 'yum groupinstall "KDE (K Desktop Environment)"'. That detected the need to install kdeaccessibility and im-chooser. After it did so, I restarted X but the focus problem remains.