Hey mtkang,
I use Quicktime Pro to build my timelapse's along with Final Cut Pro 7. The workflow is as follows:
What I do is assemble my timelapse with quicktime pro and keep it at the native resolution the images were shot in. Export it to an intermediate codec (ProRes or Avid's DNxHD will work fine) at the images original resolution. This will give you a large file with a high-resolution, of course, unless you have a top of the line computer don't expect to even try to playback this file smoothy.
You then take that file and import into your NLE, in my case it's Final Cut Pro 7. I create a 1920x1080 progressive timeline. I throw my large timelapse file that quicktime pro has made, into my timeline. Because our file still has that large resolution we are able to do some pan's and zoom's within our timelapse to create a more interesting composition if desired. You can or even add some effects or color styling. Render your new timelapse and export it at 1920x1080. This will give you a beautiful timelapse that should be able to be played back just fine.
The method I describe above is explained in a wonderful tutorial by Philip Bloom that you can watch it here:
.
You can see an example timelapse with effects that I've made using this method by visiting
http://julianmeli.com/Aruba-Photo-Fun (the timelapse video is embedded near the bottom middle of the page).
Best of luck & Keep Shooting!