Eagle, I never got that scientific determining what was wrong with any sign ballasts. Usually, it's bad lamps or ballast. Shorts are very, very common in signs because they're never really watertight. Vertical is a bad position for lamps in signs because water will enter eventually, travel down the lamps to the bottom sockets and well up. One socket can knock out the rest, usually on the red lamp leg as I remember, so I'd change any burnt ones.
That 6" of water in the lamp got there via a heat crack in the glass at the bottom of the socket most likely. The lamp has negative pressure, a vacuum, and literally sucked up the cool water that cracked the glass to begin with. The ends of the lamps get hot and when cool water comes into contact it fractures.
Andy