I have a relatively-large folder of images that I haven't added to iPhoto. They all had custom thumbnails, which made browsing them via Cover Flow quite disgusting.
If you want, make a quick run to the Terminal, and use these two commands, which will strip an entire folder's worth of JPEG, GIF, and PNG files of their thumbnails:
cd ~/Pictures/or
wherever_your_images_maybe/
sips --rotate 360 *
After this, Cover Flow started to actually read the files, and now I can flip through my images beautifully.