Strange rendering of tools in the hotbar of HD texture packs

In the pictures I am using faithful 64x64, however I have also noticed this on BDcraft and Soartex Fanver. As you can see it looks like a chunk is taken out of the tool, however the ingame texture shows no such thing, it seems to only affect thin textures like tools, sticks and blaze rods.. I did not notice this in 1.4.7.