From what it sounds like, I'm fairly sure the problem is that your logo's alpha channel is completely white or nonexistent.
In photoshop, open the
Channels tab and turn off RGB/red/blue/green and turn on the channel that should be labeled
Alpha 1. If it is completely white, that means that the entire canvas of the image is set to be visible, transparent background or not. (on a side note, if it were completely black that means the entire thing would be set to be transparent)
White on alpha = visible pixels
Black on alpha = transparent pixels
Assuming that the alpha is a completely white fill, the fix is pretty simple. First thing you'll want to do is fill the alpha channel with black. This will render the entire image transparent ingame.
If you have your logo on its own layer, all you need to do is right click on it in the layers pane and select "Select Pixels", which as it would suggest, selects all active pixels on the selected layer.
That being done, go back to "alpha 1" and fill in the selection with white - this will make only the selected portion of the image visible ingame. Save then re-import into the client, and, if I'm right, it should show up correctly.
That's only my guesstimate, it's totally possible the problem lies elsewhere but that is what it sounded like from what I was reading. If I'm wrong, please provide a screenshot and maybe the .tga files and I can take a closer look
*EDIT*
If it helps at all, here's a visual example of how ShaiyaX's login logo looked as both the canvas and the alpha: