Thinking about this last I came up with a couple of questions that might help me diagnose this:
1) Is there anything I should be able to see on the valves that indicates whether they are opening and closing?
2) If I put the boat on the trailer, will I be able to remove the brass mushroom cap on the intake so that I can see if anything is plugging it up? Or is it glued to the hull?
3) If the internals on one pump failed, could it prevent the system from filling and draining as it should? I'm not at the boat right now, but I think the system works by passing water through the fill pump in order to drain. If the fill pump failed, (and by failed I mean exploded internally) that would explain the poor fill time, and if by failing its created a blocked passage way, this could also explain why it won't drain. If anyone with more experience with the ballast system wants to chime in on this thought I'd like to hear it.
I'm still hoping its just something plugged in the intake. Im considering putting on some goggles and swimming under and trying to fish it out with a coat hanger.