Where is your atlas file located at? Did you put it under your mod's GUI folder? (Public/MyModName_GUID/GUI).
Also, your PNGs do not need to be included in your mod. They can be located anywhere - The reason we need them is just for the Texture Atlas editor, to add entries with the right names and in the order your texture was packed.
They could be blank image files and it would still work, because all it's using when you add an entry is the name of the PNG, and adding them all at the same time ensures it adds them in the right order.
