Why dont you compress them directly in ae*? I mean one less step to go wrong.
Anway it has been gone over and theres no way we can bedug your thinking flaw with the data you provide us.
You should do as i told and ask giantlizard for the AE project he was using to fix your problem the first time and use that as a basis for redesiging your workflow.
*or why do you make a animation out of it in ae? Why nbot just rad the roiginal fromaes in quicktime directly if you MUST use quicktime.
Anyway do NOT use a preset prject type in after effects, because its the worng kind of preset most likely set ALL OPTIONS anew form scratch. Seems to me your assuming interlaced content which it isnt offcourse.