Dykam

If you look closely you can see a piston block with invalid ID popping up. This could potentially also be a transmutation bug.

@insomnica_lemon This also explains why it 'fixed' itself when breaking blocks. The breaking particles did so.

I guess an, eh, hotfix is spamming torches or fires.

@insomniac_lemon
I added a dirty solution here, which processes all .png's in a resource pack: http://www.reddit.com/r/Minecraft/comments/1o5991/minecraft_snapshot_13w41a/ccow741

It doesn't just half, it inverses the blending operation `a + a * (1 - a)`-> `1 - sqrt(1 - a)`. Downside is that it increases the amount of pixels below the threshold.

It seems to be indeed. However I never experienced it in previous snapshots, it seems much more severe now. And for him it seems to be happening at distances, here it just stays like this until you break a block. And the cut-off point seems 90% now, default water texture became completely transparent, not partially.

It now happened on two separate servers for me, regenerating an entire chunk.

Please edit the title so it describes the bug, for example "Villager disappears when exiting a minecart"

There is not enough information in your ticket to resolve the issue. Chunk errors happen, and to fix them you need to offer details to reproduce it accurately.