I am using the following command on Ubuntu 13.04:
./bin/etcpack file_name.png folder_name -s slow -c etc1 -e perceptual -f RGB -aa
which should generate an etc1 atlas with alpha channel included bellow the rgb image.
When alpha channel is 0 or 255 in original image, the result image is fine, and the alpha image contains in all channels a value identical to alpha in the original image.
When it has intermediate values, then I get in result image smaller alpha than in the original, something like ~ alpha_original/3, but it is not consistent.
When doing the same thing from UI, I get expected values, ie original alpha is replicated in all channels of alpha image.
Is it a bug, or am I missing something?