I have created 3 custom Minecraft texture packs (they are 64x64) for 1.5.2 and I used the texture ender to convert them to 1.6.1 format. the texture ender worked and some of my textures like leaves showed up as I made them, but my wood planks (all types), paintings, bark (all types), water (not flowing), wool (all types), stained clay (all types), cracked stone bricks, all mobs, chiseled nether quartz, and a ton of other blocks are stuck as default. In addition, none of my animations work- flowing water, tree bark, beacon, etc. show up as either a purple and black checkerboard or as solid purple. Plus, all of my items show up as default and the chests, signs, and things that used to go in the "item" folder show up as default too. I have rechecked each and every animation in 1.5.2 and they work. I have also created 8+ copies of each of my 3 texture packs and this happens every single time.
What I expected to happen was that the texture ender would make by 1.5.2 texture packs into resource packs, I would copy and paste them into the resource pack folder, and I would happily play Minecraft.
What actually happened was I spent four hours testing blocks and re-using the texture ender again and again and again only to find that my texture packs STILL do not at all work.
I opened the texture ender in Java SE platform Binary, went to the flash drive that I keep my texture packs on, and clicked on them. I then copied the new resource pack into my .Minecraft resourcepack folder and opened them in Minecraft 1.6.1.
also WHY did they change the texture pack format from 1.5, it was very simple and easy to understand. 1.6.1 just wastes a big chunk of my day and screws up my texture packs. I would attach the texture packs but there is not enough room.