Waterfall_13, can you share a screenshot of the alpha channel? Maybe the problem is just with it?
I suspect that the alpha channel was not drawn correctly. However, I might be wrong.
How did you create the alpha channel? Did you select the black areas in the image and fill them with a solid color on the alpha channel?
If so, try this instead: simply copy the original image and paste it onto the alpha channel. It will become black and white on the alpha channel. Then, adjust the brightness to your liking.
Added 10 minutes later
There is another option: you might need to edit not the image export settings, but the xdb file that controls the texture or material. I don't remember exactly, but there was a function there that controlled the actions with the alpha channel. And there are different values, including normal transparency processing or just a hard "visible/not visible" setting. You need to look and compare how these xdb files are configured for different materials and textures.
The Archangel's Sword and, I think, the Inferno horses have fire textures without an alpha channel... I remember spending some time figuring this out, but as usual, it turned out to be very simple - you just need to save it in the correct format - the DDS plugin can definitely do that!

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Неудачное планирование ведёт к неудаче ...
NCF - мод, добавляющий дополнительных существ в HeroesV 3.1