From: Brandi Lane
OK, I'm begging for help here. I'm having some serious problems with photoshop CS2 and multiple alpha layers.
Of course you are. Since there's no such thing as an "alpha layer", it would be impossible not to have problems trying to make them. If you want to talk about alpha CHANNELS though, let's do that.
From: Brandi Lane
I certainly know how to create an alpha layer.
You do? I don't. I also don't know how to extract green cheese from the moon, how to breed chocolate cows for chocolate milk, or how to turn lead into gold. If you figure any of those things out, be sure and let me know. In the mean time, let's talk about things that actually do exist, alpha channels, not alpha layers.

From: Brandi Lane
I know how to make multiples of them and turn them on and off with the little eyeball thingamabob. Where I'm getting balled up is that it seems that when I save to any flat file, it does not matter which layers I had visible at the time of save, they are all binary OR'd together (if any pixel in any layer is white, then the result is fully visible alpha) whether or not that layer was enabled at the time of save.
Am I losing my mind?
I'd really like to help you, but I'm sorry to say I'm having a very difficult time figuring out what you're talking about. First, what does "all binary OR'd together" mean?
Second, are you in fact actually talking about multiple layers or multiple channels? The answer to that will make all the difference in the world toward solving your problem.
If you are talking about channels, then the behavior you describe would be normal. If you've got more than 4 channels in your working image, then a TGA outputted from that image will be reduced to 4, as that is the maximum number of channels that the TGA format supports. The first three, which always govern color, will be left in act, and the fourth, the one that governs transparency, will be created by compositing all the extra channels together. In such cases, Channel 4 will always come out completely white, ALWAYS.
To prevent this and other problems from happening, make sure you always have one, and only one, (properly created) alpha channel in place at the time of TGA output. Never try to put more than 4 channels into a TGA.
And remember, as you discovered, it doesn't matter whether a particular channel happens to be turned on or off in the GUI at the time of save. If it is present, it is part of the image, period.
If you are talking about layers though, then I'm afraid you'll need to re-explain what you mean in terms we can all understand.
Third, when you say "save to any flat file", do you mean you're flattening your layered images prior to save, or are you simply noting that TGA files are inherently flat? If it's the former, stop doing that. It's destructive and it yields no benefit whatsoever. Always preserve your layered work as a PSD first, and then save out to TGA as a copy afterwards.