Transparent Textures are Broken At Certain Transparencies

My custom resourcepack's water texture files worked fine in Snapshot 13w37b and now are broken, as in it has some parts of the texture missing.

My water_still.png has holes in the texture, water_flow.png has basically the opposite look of water_still.png.

EDIT: 13w41a - Flowing/still water are still broken at a distance.

EDIT: 13w42a - Everything appears to be fixed from what I've tested. Please post your feedback from the new snapshot.