I can confirm that this still happens with the latest version (as far as I know) of TextureEnder.jar, as well as the 1.6.2 prerelease.
Edit: This is also happening for me with texture packs that I have unzipped to convert, then rezipped to use.
Jensen Krone
I can confirm that this still happens with the latest version (as far as I know) of TextureEnder.jar, as well as the 1.6.2 prerelease.
Edit: This is also happening for me with texture packs that I have unzipped to convert, then rezipped to use.