Is there more than one method of making something transparent? Also, is that the ground under it, or a floor that is technically not the default “ground” or whatever (I’ve never made a HL2 map, only failed to make a HL1 map)?
Make some other simple objects and see if they’ll do the same, both with and without that texture, also, try changing the textures on your model and see if that fixes it.
However, what I’m seeing there doesn’t look like transparency, but rather an error where it’s rendering faces of the object even if they’re obscured behind another one, or that the one texture is being rendered “over” everything else. Put another random prop in the room and see if you still see those faces of the object through other objects.