I use .obj files exclusively. If your texture has an alpha channel, then it will cause the model to be transparent in 3DGS, unless you give it a shader that uses the alpha channel, like mtl_specBump. mtl_specBump uses the alpha channel as the model's specular map. Otherwise it will control transparency by default.

If you still have any trouble, feel free to message me with a link to download the blenderfile. I use 2.76 right now.