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Recent versions of ImageMagick do not assume a 4th channel means its alpha. To specify an alpha channel you need to set the TIFF extra samples attribute and declare it pre or unmultiplied alpha. Post a URL to your image here and we will verify if that is the problem with your image.
As mentioned, the problem is that the extra samples are not specified as associated or unassociated alpha. See http://www.awaresystems.be/imaging/tiff ... mples.html
. It states
If an extra sample is used to encode information that has little or nothing to do with alpha, ExtraSample=0 (EXTRASAMPLE_UNSPECIFIED) is recommended.
However, even the TIFF library has a workaround for folks that do not honor this field. We will get this patch into the latest ImageMagick development release.