Let's start with a potential terminology issue.
Are you using the "Render Queue"?
You should be. You should not be using the "Export" function under the File menu.
Various codecs will yield different results. Uncompressed is a very good one if you want to maintain true-to-source quality.
What is the final destination for your project? DVD? Web?
This will help determine the codec you'll want to use.
You didn't say how your colors don't match. I'm going to guess that it's a gamma shift, because QuickTime has known problems in this area. See "QuickTime and gamma in non-color-managed projects".
Of course, the real answer to making colors consistent is to use color management.