When i run the texturepacker in libgdx i have the problem that it doesn't pack all the images in one big sprite sheet. If i for example have 4 images and it only packs 3 of them. Note that 2 images are the exact copies of eachother so maybe that has something to do with it.
LibGDX by default doesn't pack images which are exact copies. This can be overridden by setting alias to false in your configuration.
alias: If true, two images that are pixel for pixel the same will only be packed once. (default: true)
However, usually it is beneficial to pack the same images only once because it creates a smaller texture. You can still use both names when getting TextureRegion objects or creating Sprite.