What I would recommend is, if you want pink as the tileset's transparent color, then make it the second color in your palette. Just to be extra sure you're doing it right, that specific shade of pink should be used in exactly one index of the palette.

If you're (still) using TilesetPal, before the color reduction you can change the second index to pink and mark it as "Don't Change." You'll have to do something similar to this for your textured background by the way.
(this is where a link to DTR would've been particularly useful)

Also, you can't use solid black (#000000) as it is since it will always be transparent. If you want to use black, use a color like #000001 instead.