Getting a "cannot open" error when saving does seem weird.

Where did you save the .png in any other editor before trying to pcx it? The tileset extractor definitely shouldn't output a 24bit png (JCS won't accept image files with their depths different than 8bit = 256 colors).

Also, the Automask option will make all pixels that don't use a transparent color masked, which I suppose is not what you're looking for. You'll need to use the original mask image, and afaik you'll need to set its depth into 8bit rather than 2 colors.