Description of problem: If I start any application, the apps are starting under the panel, meaning if I want to move or close them, I need to hide the top pannel. If I turn off compiz the behaviour works properly.
There was a problem with the plugin responsible for placing windows not getting loaded. It should be fixed in rawhide, but you may have to issue a gconftool-2 --unset /apps/compiz/general/allscreens/options/active_plugins after upgrading to reset the plugin list.
Is this still an issue? First of all, even if the title bar is hidden by the top panel, you can drag the window around by placing the mouse cursor inside it, holding the 'alt' key pressed, clicking the left mouse button and moving the mouse. Concerning the issue you report, check with gconf-editor that the 'place' plugin is present and enabled, otherwise add it to the plugin list. Do not forget to close this bug upon success.