Are you using Compiz Fusion? There is some historic issues with the top panel 'disappearing' or taking a while to appear. Ensure that Compiz is up-to-date.
You could try removing and replacing the default top panel by typing the following in a terminal (assuming that you are using gnome). I'm not sure that this will help but it's worth a try if updating Compiz doesn't work.
gconftool-2 --recursive-unset /apps/panel