I'm trying to figure out what the problem is but you mention too many things
so I'm afraid I'm getting confused.

Could you please give a step by step example of what you are doing and what
happens when you are doing it,  so I or someone else here can help find out
what is going wrong? 


>I am using Gimp 2.67
>I am modifying textures for a video game. The video game applies a special
>effect to the areas of the texture that are not 100% transparent or 100%
>I am trying to make certain parts of the texture 100% transparent so that
>is invisible in-game and not subject to the special effect. 
>I have used the eraser, rectangular select, and free select tools, and they
>all have the same problems. 
>Basically, what happens is that the area outside of my selections or
>also seems to be affected. I have antialiasing off for the free select tool.
>have hard-edge on for the eraser, and all the brush dynamics turned off for
>it. The eraser is at Circle (05) which is a square, at the scale of 1.00 I
>have tried using Select>Sharpen
>The rectangular select tool has antialiasing checked and greyed out, so
>I cannot uncheck it. 
>I believe this was introduced in one of the most recent versions (I
>"upgraded' to gimp 2.67) as I don't remember seeing that in a version I
>to use, I think it was 2.1 or 2.2. I also don't remember having this
>with those versions.
>The areas outside of my selections and erasing are being affected, so that
>in-game the special effects are applied to areas I don't want them to be. I
>have looked in the alpha channel, and there appears to be no actual
>transparency in those areas, it seems to be solid black. 
>Is there anyway to ensure that the areas outside of my selections will not
>Also, I would like to know how to copy the exact alpha channel from one
>to another image, without the original alpha channel being changed. I have
>tried doing this before but the alpha channel always looks different when
>pasted into the second image.

jolie S (via www.gimpusers.com)
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