Since 13w38a custom rain texture's pixels with alpha value (opacity) of 10% of lower turn completely invisible, showing up only at opacity 11% or more regardless of video options (I tested at Fancy, render distance 6, max smooth lighting, moody brightness, no mipmapping/shaders). I didn't test snow texture.

The following pictures were taken with a test texture (2 vertical white lines at fixed opacity): the first one in 1.6.4 at 10% opacity displays correctly; the second one in 13w39b disappears; the third one has 11% opacity and shows up again.