Questions and postings pertaining to the development of ImageMagick, feature enhancements, and ImageMagick internals. ImageMagick source code and algorithms are discussed here. Usage questions which are too arcane for the normal user list should also be posted here.
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The reason it happens is that GIF only supports one transparent color whereas many images have a variety of transparent values ranging from 0 to 255. Since transparency is binary we choose values from 0 to 127 as transparent and values from 128 to 255 as opaque. A future version of ImageMagick will permit you to specify a specific color as transparent instead of it deciding based on the alpha channel.
See http://www.cit.gu.edu.au/~anthony/graphics/imagick6 for a discussion on how to make transparency work properly with GIF images and why GIF is a bad choice for transparent images and how PNG is the preferred choice.