First off, much thanks to Skeeler for donating some old ballast timers for experimenting with!
I finally have a ballast timer solution that works. After a few beers and some reverse engineering, I was able to rewrite the firmware that controls the ballast timer. I got rid of all of the crappy logic that they tried to use to detect when the tanks are empty. They now work as a timed switch that will fill/empty for a set amount of time then turn off. No more turning them on only to have them shut off after 5 seconds.
Now, to reprogram them is not for the feint of heart. You need to pull the timer box, remove the modules, take the modules apart, connect a programmer, reprogram, then reassemble. It also requires a special programmer and the correct firmware file. But, if anyone on here is as big of a geek about this stuff as I am, you have the tools and you want to reprogram your timers, let me know, I'll send you the file and tell you how to do it.
Here is a picture of the setup I used but you can use other programmers also.