Some shaders, such as Poiyomi, use packed images (RGBA channels) for various data such as reflection, AO, specular, smoothness, etc. If you notice weird artefacts on the alpha channel then you might need to uncheck the “Alpha is Transparency”-option.
For example, if you notice the following:
You can turn it off here, with the following result:
My guess is that alpha as transparency will cause a compressed texture to treat the alpha channel as well… transparency. If something is fully transparent it doesn’t have a colour and thus it will optimize away potential useful data!