I was able to "fix" my resource pack by saving the icons.png gui file in an 8 bit format (Using Paint.NET) which fixed the alpha channels.
So it seems that this is indeed a problem with how MC handles the alpha channels now.
I am also having this problem. Doesn't happen with the old launcher, presumably because older LWJGL.
I can confirm this as well. Binding the "NONE" key to anything else fixes the problem.
I was able to "fix" my resource pack by saving the icons.png gui file in an 8 bit format (Using Paint.NET) which fixed the alpha channels.
So it seems that this is indeed a problem with how MC handles the alpha channels now.