I have looked through the bug reports here and nothing fits exactly to this issue.
The past couple of versions of CV 1.26.2.10 through to most current. Also 1.26.3.1 & 1.26.3.2 are affected.
The issue: I've noted that any texture which contains Alpha renders as Black, identical behaviour if you had edited the texture and set colour to Black (although this is not the case) as it applies to all alpha's. In order to have the Alpha render properly, you have to edit the object and turn on Full Bright in order to properly see the textures.
I have tested with Imprudence Beta-2, MeerKat and most current Linden Labs Development and these viewers all render the Alpha properly, without having to be on "Full Bright". My Graphics & Network Settings in particular are exactly the same for Cool Viewer & LL Dev Viewer and as close as possible with non-v2/3 based viewers.
This behaviour is identical in SecondLife & OpenSim.
CV Before Full-Bright:
http://imagebin.org/194885CV After Full-Bright:
http://imagebin.org/194886LL Dev Viewer (no full bright, normal)
http://imagebin.org/194889Viewer About info: