No I think everything needs alpha, so normally when you draw something in additive mode it already has alpha and caps at 1, so most things will appear normal, if you set alpha to zero (in add mode) it will add zero alpha, resulting in completely transparentness, it could depend what alpha has been set before hand to those pixels, so if your using a surface\layer thats filled with zero alpha, (like when you do draw_clear_alpha(0, 0) no alpha gets added, the rgb values still might, but they wont show up without some alpha added, I was gonna say the solution would be to do draw_clear(c_black) so its got full alpha, but it seems like that surface your using needs alpha, I don't know tho, I don't know what your setup is like,
I just know that if you've got a zero alpha surface to begin with: draw_clear_alpha(c_black, 0), and in additive mode, your gonna need to add some alpha to the pixels before they show up anything, that still doesn't explain the problem with the highlighted squares, sorry! but I feel its something to do with those things I mentioned