What resolution and codec are your source files? Are you correctly interpreting the field order of your source files? Are you rendering interlaced or progressive output? What codec are you rendering your output files to? ("Quicktime" and "WIndows Media" doesn't tell us anything.)
Can you explain what is wrong, SPECIFICALLY, with your output. Or better, post an image.
The first image is a screen shot of the original footage taken in AE. The second image is the exported qucktime. The quick time is at half size and the AE is 50%. The source files are a qucktime output of a frame by frame animation I created in AE. I have tried rendering both interlaced and progressive. My instructor had me drop the source files onto the "Create a new composition" icon at the bottom of the project window so AE would interpret the sourcefiles correctly to be exported back to Final Cut Pro. The format options are set to no compression. I don't know how to tell what codec I am rendering to.
My instructor isn't any help since I am working on a PC. He only knows Mac.
Please be more specific. You are using compression in there, so this depends a lot on specific CoDecs and settings. Just refering to Quicktime or Windows Media doesn't mean anything with regards to data rates, compression quality settings and all that...
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There is a distinct gamma shift and visible compression artifacts in your rendered image, as Mylenium said. It's impossible to assess the problem without knowing the codecs.
Open your source footage and equivalent rendered QT file in QT player. Go to Window/Show Movie Inspector. In the inspector, you'll see which video and audio codecs are used in each file.
Inspector looks something like this: