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.