Last time I ran ZA on my priest was doing mass dispel on party for bear phase of ZJ fight. I cast MD with about 3 seconds left on timer. It hit, then immediately a new paralysis showed up on my buff/debuff display (with appx. a 3 second count down). Apparently it affected others because several people got paralyzed.

What do you mean "3 seconds left on timer"? When I do it, I wait for the raid warning, then press my MD key and aim the AOE circle. When the debuff lands on me, I click to cast it and 1.5s later we're all good. I understand you've had some trouble with too many targets (hunter pets) - I would suggest having somebody (perhaps the hunter themselves) stand outside of MD range in that case to control who doesn't get cleared.

Also, if you have a tankadin, make him work overtime and dispel himself + one healer, just to be sure =)

I was slow on the first MD cast, and started it with 3 seconds on timer. The MD landed. Immediately after the MD landed, the timer reappeared with 3 seconds on it. I can't explain it, maybe too many targets, I don't know.