I've noticed that F@H does some very strange things with the system tray. If you click on it to see the display it often screws up all the tooltips. I assume it is somehow messing up the handles (what windows uses to identify resources) so you get the tooltip associated to a different prog.
It is probable that when your other prog has closed, it has sent a message to windows asking for it's icon to be removed from the system tray. But if the handles are messed up it is likely that it has inadvertently asked for a different icon to be removed, in this case the F@H icon. Subsequently, windows notices that the owner of the correct icon has gone away, so windows removes that icon too.
Can't be sure this is what is happening, but it is a reasonable guess.
No need to reboot, simply stop the task from within task manager then start it again from your start menu (presumably it is in Programs/Startup).