Drop in layers visual quality when I change comps size -WHAT???

Hi there! So check this out. I import a progressive frame quicktime movie into AE, drag it to the new comp button in the project window and a new comp is created matching the specs of the source material.
But as soon as I change the size - width and height - of the comp in the composition settings window, the visual quality of the quicktime in the comp degrades dramatically. it's like someone dropped a fast blur on it with a value of around .5 or 1. Any ideas on what the heck is happening?
working on a 2 x 3 GHz Quad-Core Intel Mac running 10.4.11
9 GB 667 MHz DDR2 ram
Radeon X1900 w/512 MB video ram
1 TB raid
After Effects CS3 Professional vs 8.0.2.27
Quicktime 7.4.5

David & Mylenium,
I should have been more specific. Sorry. This is what's happening. The source is a 1920 x 1080 sq. pixel Apple ProRes 422 quicktime. I bring the footage into AE, key it and then prerender it.
Then I create a new comp (by dragging the footage to the new comp button) based on this prerendered footage. I do any compositing/etc i need to and then I take this final comp and render a master quicktime. Finally, I wait for my designers to tell me what size dimensionally they want the video to be ( it goes to FLV).
Once I get this info, I create a new comp one of 2 ways....
1. I drag the master quicktime to the new comp button, it makes a new comp (everything still looking fine) and then I change the dimensions of the comp to fit the designers request. As soon as I change the dimensions of the comp - the video looks like garbage. it looks like it's been slightly blurred - before and after I've scaled it down to fit the new size of the comp.
2. Sometimes I create a new comp with the dimensions the designers requested and then drag the master quicktime into it. Same thing. Blurred/bad footage before and after scaling to fit.
What in the heck is going on? Is there some strange ratio between height and width AE has to have? My footage is SQ PIX so... what the heck?
So David, when you ask if my footage is scaling to match the new comp size, the answer is no. If my footage is 1920x1080 and the final comp size is 400x340, I scale the video down so that all the action/movement of the actors fits into this size.
Mylenium, my footage and comps are SQ PIX and its the same with both OpenGL on and off. As far as for the codec, I see this with my original codecs - both DVCPro-HD and Apple Prores 1920x1080. I also see it happen with the prerendered qt's that have animations codecs.
I'm sorry for the long post guys. It's just been thoroughly frustrating. This footage should stay sharp. Sometimes it does. Sometimes it doesn't. It's very strange. I've trashed prefs, reinstalled, retraced my steps and found nothing.
Time to pull my hair out. But thanks for your responses though!!

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