I know what you're saying... which is why this sounds so bizarre. It's almost like the thumbnails crops are slowly deteriorating. The ones I just did last week are fine.
but, check out these from about 5 months ago:
http://www.phlumf.com/gallery/central-california/sierra-nevada/
If you see the few thumbnails with the black edges, that's because all my photos have a black border in the .jpg. But, when I create my thumbnails, I never include the black border. While it's hard to remember exactly how I cropped them, I'm pretty sure these aren't what I did.
I agree it sounds like voodoo or something. It just doesn't make technical sense. But, I thought perhaps there was some obscure bug... or maybe I'm just going mad.