If you use Tileset Extractor, the mask picture it produces uses two palette indexes, 0 and 1, both of which are treated by JCS as transparent (i.e. non-solid in case of mask) when building a tileset. You will have to modify the picture to use a different palette entry for solid parts. Depending on your image editor of choice, the easiest way to do it may be to apply a palette that contains the transparency purple at index 0, black at index 16, and white everywhere else, while maintaining nearest color matching. Although if your image editor supports palette-based color replacement, that should be simpler.

I haven't done this for a while so if that fails, you may also want to look into replacing color #000000 (black) with another color. I can't remember right now if JCS has any special treatment of black.