When using my custom Resource Pack there happens a strange alpha channel bug. In the attachment you can see that it's creating black spots, instead of transparent. On default textures the bug is not met.
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Strange, after some changes and packing it into a zip file I am unable to reproduce this bug. Maybe it's because I had earlier a temporary folder in the non-ziped version.

Please do not mark issues as affecting future versions, as you could not have tested those.
Going to assume it was an issue with two programs trying to access a file at the same time.
After some time messing around the same issue happened. After removing barely everything I've attached my texturepack.
Still happens in the newest 13w41 snapshot and looks even worse..
[EDIT] OMG I don't get it, now after some time fiddling with other things in the resource pack the bug doesn't appear anymore.. This is really confusing :|
When changed to the newest snapshot, the bug isn't happening, time to look what will happen after some time fiddling around with my Resource Pack 🙂

Is this still a concern in the latest Minecraft version 13w48b? If so, please update the affected versions in order to best aid Mojang ensuring bugs are still valid in the latest releases/pre-releases.
No sir this one is fixed for me! Thanks Mojang team, if it would come back some day I'll ask for reopening
Please attach your resource pack.