Running the TextureEnder.jar against a zipped texture file is only converting the .txt files to .mcmeta.
It doesn't convert the filenames to the new file format nor does it move the files to the new folder format.

Examples:
"beefcooked.png" is not renamed to "beef_cooked.png"
"kz.png" is not renamed to "paintings_kristoffer_zetterstrand.png"

"chest.png" remains in the item folder and is not renamed to "normal.png" and is not moved to the chest sub folder of the entity folder.

The above are only a few examples.

I'm not sure if the tool is meant to rename/move the old 1.5.2 format textures - so please tell me if I'm expecting too much, but I suspect a lot of people will be experiencing this issue soon enough.

It works well enough on an unzipped texture pack though ;p

Thanks for reading.
Vlad