yep makes sense, because the command block gets powered when you turn the clock on, but is constantly receiving one signal instead of pulses.
I used mcedit to make the BIG ceiling. But all was fine then. I then added the zombie spawners with mcedit, and they worked fine. But then I noticed that they stopped spawning monsters as I manually built the ceilings on the glass spawning rooms. After I built the smaller iron ceilings on the 4 spawning rooms BY HAND, the whole room suddenly got bright. Strange.
Oh that makes so much sense! Thanks Avstar98