It sounds like they’re being drawn transparent, but the background is the default black. Have you tried drawing something behind them to see whether they’re actually black, or transparent?
If they actually are black, it may be that your library is ignoring the tileset’s alpha channel, which is probably an option you can tweak somewhere. A way to check whether the alpha channel is being ignored is to use a semi-transparent white tile. If it turns out completely white in-game, the alpha channel is being ignored, but if it turns out grey, then you’re just rendering on a black background and the alpha is correct.