What is the size (pixels WidthxHeight) of the source picture.
Just to give you one example of something that can happen...let's say you have an image that is 25 wide and 100 high. Lets also say that under appearance options you have the thumbnail set to 100 pixels. The setting in appearance options is for width so it would make the picture 100 wide and 400 high but would not mess with the picture in detail images. If I got lucky on the first try than I do have a solution. I have had this problem and fixed it with Fireworks. I opened the picture in fireworks and changed the canvas size to width 100. I then made the canvas color the same as the page color in your store (white for most that I have seen). This will keep the picture the same size for the thumbnail as you have made the width the same as the setting in appearance options.
This is just one possible scenario that I can think of.
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