Edited photos pixelated in cover flow preview...

I recently bought a Nikon D90. The images are pristine, but I like to correct the color of every picture I shoot using Photoshop CS4 and then import the corrected image into Aperture.
My problem is that when I correct the color using AutoLevels in Photoshop, and then view the image in cover flow, the preview is smaller and very pixelated. I'm able to open the photo in Preview, but the cover flow preview's quality is horrible. This was never a problem with image files from any of my previous cameras.
I've tried to see the differences between the specs on the two files, but can't see any. I'd like to understand why this is before I start making changes to all of the files I shoot with the new camera. My hope is that I won't create a bigger problem once the files are in Aperture.
Any help would be much appreciated.

I'm sure my workflow is far from professional. Aperture certainly does non-destructive editing, but I'm using it for cataloging more than editing. I've been using Photoshop longer and trust my skills with it more. However, using an external editor with Aperture results in the application creating a huge secondary edit file (I think it's a PNG file, but don't quote me). Rather than create that large unnecessary file, I'd prefer to import a file that I've already correct once. If I want to work with the image later, I export a new image from Aperture and work from there.
I'm shooting in JPEG (again, I'm far from professional). I don't know that I'm doing the right thing here, but I don't want my lack of knowledge to compound my problem by importing an image file I've messed up somehow.

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