Quicktime remembers your export settings from one export to another. Therefore, you must now change your settings before exporting your flattened composite. You don't have to change the compression settings, if you don't care that the file will be rather large, but you must click the Filter... button and select "None", at the top of the filter list, so that no filters are applied to your final clip. If you are working with a standard, mini-DV camcorder, you'll probably want to export using the DV/DVCPRO codec. If you are making an HD movie, or you need to preserve more quality, you can select an HD codec, or stick with PNG for lossless compression.

Once your settings look like the ones shown below (no filter selected, proper compression, etc.), click Ok.